diff --git a/tools/moltemplate/LICENSE.TXT b/tools/moltemplate/LICENSE.TXT new file mode 100644 index 000000000..c8c1ec081 --- /dev/null +++ b/tools/moltemplate/LICENSE.TXT @@ -0,0 +1,28 @@ + +Author: Andrew Jewett, Shea Group, http://www.chem.ucsb.edu/~sheagroup/ +Copyright (c) 2013, Regents of the University of California +All rights reserved. +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + * Neither the name of the University of California, Santa Barbara nor the + names of its contributors may be used to endorse or promote products + derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF +THE POSSIBILITY OF SUCH DAMAGE. + diff --git a/tools/moltemplate/README.TXT b/tools/moltemplate/README.TXT new file mode 100644 index 000000000..2e73b6374 --- /dev/null +++ b/tools/moltemplate/README.TXT @@ -0,0 +1,61 @@ + -- Description: -- + +Moltemplate is a cross-platform text-based molecule builder for LAMMPS. + + -- Typical usage: -- + +moltemplate.sh [-atomstyle style] [-pdb/-xyz coord_file] file.lt + + -- Web page: -- + +Documentation, examples, and supporting code can be downloaded at: + + http://www.moltemplate.org +The most up-to-date version of moltemplate can be downloaded here. +(After download, you can unpack the archive using: + tar xzf moltemplate_2012-3-31.tar.gz +The date will vary from version to version.) + +---------------------------------------------------- +---------- INSTALLATION INSTRUCTIONS: ------------ +---------------------------------------------------- + +This directory should contain two folders: + src/ <-- location of all python and bash scripts + common/ <-- location of shared force fields and molecules + +The ``moltemplate.sh'' script and the python scripts that it invokes are +located in the ``src/'' subdirectory. You should update your PATH environment +variable to include this directory. + +If you do not know what a PATH environment variable is, read: + http://www.linfo.org/path_env_var.html +(I receive this question often.) + +It is also a good idea to set your MOLTEMPLATE_PATH environment variable to +point to the ``common/'' subdirectory. +(Force fields and commonly used molecules will eventually be located here.) + + -- Installation example --- + +Suppose the directory with this README.TXT file is located at ~/moltemplate. + +If you use the bash shell, typically you would edit your +~/.profile, ~/.bash_profile or ~/.bashrc files to contain the following lines: + export PATH="$PATH:$HOME/moltemplate/src" + export MOLTEMPLATE_PATH="$HOME/moltemplate/common" +If you use the tcsh shell, typically you would edit your +~/.login, ~/.cshrc, or ~/.tcshrc files to contain the following lines: + setenv PATH "$PATH:$HOME/moltemplate/src" + setenv MOLTEMPLATE_PATH "$HOME/moltemplate/common" + + -- Requirements: -- + +Moltemplate requires the Bourne-shell, and a recent version of python +(2.7, 3.0 or higher), and can run on OS X, linux, or windows (if a +suitable shell environment has been installed). + + -- License: -- + +Moltemplate is available under the terms of the open-source 3-clause BSD +license. (See LICENSE.TXT.) diff --git a/tools/moltemplate/common/amber/README.TXT b/tools/moltemplate/common/amber/README.TXT new file mode 100644 index 000000000..3d1739801 --- /dev/null +++ b/tools/moltemplate/common/amber/README.TXT @@ -0,0 +1,27 @@ +This directory contains scripts used for converting AMBER parameter files +into moltemplate (.LT) format. When a newer version of the AMBER parameters +is eventually published, you can use these scripts to convert the new files +again. (Some tinkering may be necessary.) + +The main bash script is a wrapper which simply splits up the parameter (".dat") +file into fragments which (it thinks) correspond to the mass, pair, bond, +angle, dihedral, and improper section of the original .dat file. +(However sometimes it gets this wrong and you have to split it up manually!) + +Then this bash script invokes the relevant python script to convert +each section into .LT format: +amberparm_to_mass.py +amberparm_to_pair.py +amberparm_to_bond.py +amberparm_to_angle.py +amberparm_to_dihedral.py +amberparm_to_improper.py +In case this goes wrong, you may have to run these scripts manaully. + + +Find out how to run this bash script by invoking it without any arguments: + +./amberparm2lt.sh + +-Andrew +2013-8-04 diff --git a/tools/moltemplate/common/amber/amberparm2lt.sh b/tools/moltemplate/common/amber/amberparm2lt.sh new file mode 100755 index 000000000..d27897a7b --- /dev/null +++ b/tools/moltemplate/common/amber/amberparm2lt.sh @@ -0,0 +1,203 @@ +#!/bin/sh + +if ! which amberparm_mass_to_lt.py > /dev/null; then + echo "\nError: \"amberparm_mass_to_lt.py\" not found. (Update your PATH?)\n" >&2 + exit 2 +fi +if ! which amberparm_pair_to_lt.py > /dev/null; then + echo "\nError: \"amberparm_pair_to_lt.py\" not found. (Update your PATH?)\n" >&2 + exit 2 +fi +if ! which amberparm_bond_to_lt.py > /dev/null; then + echo "\nError: \"amberparm_bond_to_lt.py\" not found. (Update your PATH?)\n" >&2 + exit 2 +fi +if ! which amberparm_angle_to_lt.py > /dev/null; then + echo "\nError: \"amberparm_angle_to_lt.py\" not found. (Update your PATH?)\n" >&2 + exit 2 +fi +if ! which amberparm_dihedral_to_lt.py > /dev/null; then + echo "\nError: \"amberparm_dihedral_to_lt.py\" not found. (Update your PATH?)\n" >&2 + exit 2 +fi +if ! which amberparm_improper_to_lt.py > /dev/null; then + echo "\nError: \"amberparm_improper_to_lt.py\" not found. (Update your PATH?)\n" >&2 + exit 2 +fi + +SYNTAX_MSG=$(cat < gaff.lt + + You can also try: +amberparm2lt.sh parm94.dat "AMBERFF94 inherits GAFF" > amberff94.lt + (However, this later usage may not work. + You may need to manually split the .dat file and run these scripts instead: + amberparm_pair_to_lt.py, amberparm_bond_to_lt.py, amberparm_angle_to_lt.py...) + Be sure that all of these .py files are in your PATH as well.) + +EOF +) + +if [ "$#" != "2" ]; then + echo "${SYNTAX_MSG}" >&2 + echo "" >&2 + echo "Error: This script requires two arguments," >&2 + echo " 1) the name of the amber parm file to be converted (eg \"gaff.dat\")" >&2 + echo " 2) the name of the moltemplate object to be created (eg \"GAFF\")" >&2 + echo " (This may include the \"inherits\" keyword and parent classes.)" >&2 + exit 1 +fi + +MOLTEMPLATE_USAGE_MSG=$(cat < "${PARM_FILE}.mass" + +# The 2nd section has the list of 2-body bond force-field params +awk -v n=2 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ + < "$PARM_FILE" \ + | tail -n +2 \ + > "${PARM_FILE}.bond" + +# The 3rd section has the list of 3-body angle force-field params +awk -v n=3 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ + < "$PARM_FILE" \ + > "${PARM_FILE}.angle" + +# The 4th section has the list of 4-body dihedral force-field params +awk -v n=4 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ + < "$PARM_FILE" \ + > "${PARM_FILE}.dihedral" + +# The 5th section has the list of 4-body improper force-field params +awk -v n=5 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ + < "$PARM_FILE" \ + > "${PARM_FILE}.improper" + +# The 6th section has the hbond-parameters (no-longer used. ignore) +awk -v n=6 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ + < "$PARM_FILE" \ + > "${PARM_FILE}.hbond" + +# The 7th "section" is just a blank line. (skip that) + +# The 8th section has the list of non-bonded ("pair") force-field parameters +awk -v n=8 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ + < "$PARM_FILE" \ + | tail -n +2 \ + > "${PARM_FILE}.pair" + + +amberparm_mass_to_lt.py < "${PARM_FILE}.mass" > "${PARM_FILE}.mass.lt" +amberparm_pair_to_lt.py < "${PARM_FILE}.pair" > "${PARM_FILE}.pair.lt" +amberparm_bond_to_lt.py < "${PARM_FILE}.bond" > "${PARM_FILE}.bond.lt" +amberparm_angle_to_lt.py < "${PARM_FILE}.angle" > "${PARM_FILE}.angle.lt" +amberparm_dihedral_to_lt.py \ + < "${PARM_FILE}.dihedral" > "${PARM_FILE}.dihedral.lt" +amberparm_improper_to_lt.py \ + < "${PARM_FILE}.improper" > "${PARM_FILE}.improper.lt" + +echo "$2 {" +echo "" +echo " # ----------------------------------------------------------------------" +#echo " # This file was automatically generated by \"common/amber/amberparm2lt.sh\"" +echo " # The basic atom nomenclature and conventions are explained here:" +echo " # http://ambermd.org/antechamber/gaff.pdf" +echo " # For reference, the original gaff.dat file and format documenation are here:" +echo " # http://ambermd.org/AmberTools-get.html" +echo " # http://ambermd.org/formats.html#parm.dat" +echo " # ----------------------------------------------------------------------" +echo "" + +cat "$PARM_FILE.mass.lt" \ + "$PARM_FILE.pair.lt" \ + "$PARM_FILE.bond.lt" \ + "$PARM_FILE.angle.lt" \ + "$PARM_FILE.dihedral.lt" \ + "$PARM_FILE.improper.lt" + +AMBER_STYLES_INIT=$(cat <0): + # sys.stderr.write('prev_n='+str(in_dihedral_coeffs[i-1][-3])+'\n') + #sys.stderr.write('n='+str(n)+'\n') + + if ((i>0) and (in_dihedral_coeffs[i-1][-3] < 0)): + + #sys.stdout.write('interation_before_append: '+str(in_dihedral_coeffs[i-1])+'\n') + assert(in_dihedral_coeffs[i-1][0] == in_dihedral_coeffs[i][0]) + in_dihedral_coeffs[i-1][-3] = -in_dihedral_coeffs[i-1][-3] + comments = in_dihedral_coeffs[i-1][-1] + in_dihedral_coeffs[i-1][-1] = Kn + in_dihedral_coeffs[i-1].append(n) + in_dihedral_coeffs[i-1].append(dn) + in_dihedral_coeffs[i-1].append(comments) + #sys.stdout.write('interation_after_append: '+str(in_dihedral_coeffs[i-1])+'\n') + del in_dihedral_coeffs[i] + + #elif len(in_dihedral_coeffs) < 3: + # del in_dihedral_coeffs[i] + else: + i += 1 + + + +for i in range(0, len(in_dihedral_coeffs)): + type_str = in_dihedral_coeffs[i][0] + params = in_dihedral_coeffs[i][1:] + params = map(str, params) + num_fourier_terms = (len(params)-1)/3 + dihedral_coeff_str = 'dihedral_coeff '+type_str+' '+\ + dihedral_style_name+' '+\ + str(num_fourier_terms)+' '+ \ + ' '.join(params) + in_dihedral_coeffs[i] = dihedral_coeff_str + +# ---- finished processing dihedral fourier series ---- + + +sys.stdout.write(' write_once(\"In Settings\") {\n ') +sys.stdout.write('\n '.join(in_dihedral_coeffs)+'\n') +sys.stdout.write(' } # (end of dihedral_coeffs)\n') + + + + + +sys.stdout.write('\n') + +sys.stdout.write(' write_once("Data Dihedrals By Type") {\n') + +for i in range(0, len(lines_gaff)): + line = lines_gaff[i] + atypes = line[:11].split('-') + atype1 = atypes[0].strip() + atype2 = atypes[1].strip() + atype3 = atypes[2].strip() + atype4 = atypes[3].strip() + at1 = atype1.replace('X','*') + at2 = atype2.replace('X','*') + at3 = atype3.replace('X','*') + at4 = atype4.replace('X','*') + dihedraltype = '@dihedral:'+atype1+'-'+atype2+'-'+atype3+'-'+atype4 + + sys.stdout.write(' '+dihedraltype+' @atom:'+at1+' @atom:'+at2+' @atom:'+at3+' @atom:'+at4+'\n') + +sys.stdout.write(' } # (end of Dihedrals By Type)\n') +sys.stdout.write('\n') + + +""" + - 6 - ***** INPUT FOR DIHEDRAL PARAMETERS ***** + + IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN + + FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2) + + IPT, ... The atom symbols for the atoms forming a dihedral + angle. If IPT .eq. 'X ' .and. LPT .eq. 'X ' then + any dihedrals in the system involving the atoms "JPT" and + and "KPT" are assigned the same parameters. This is + called the general dihedral type and is of the form + "X "-"JPT"-"KPT"-"X ". + + IDIVF The factor by which the torsional barrier is divided. + Consult Weiner, et al., JACS 106:765 (1984) p. 769 for + details. Basically, the actual torsional potential is + + (PK/IDIVF) * (1 + cos(PN*phi - PHASE)) + + PK The barrier height divided by a factor of 2. + + PHASE The phase shift angle in the torsional function. + + The unit is degrees. + + PN The periodicity of the torsional barrier. + NOTE: If PN .lt. 0.0 then the torsional potential + is assumed to have more than one term, and the + values of the rest of the terms are read from the + next cards until a positive PN is encountered. The + negative value of pn is used only for identifying + the existence of the next term and only the + absolute value of PN is kept. + + The input is terminated by a blank card. +""" diff --git a/tools/moltemplate/common/amber/amberparm_improper_to_lt.py b/tools/moltemplate/common/amber/amberparm_improper_to_lt.py new file mode 100755 index 000000000..0bf36697f --- /dev/null +++ b/tools/moltemplate/common/amber/amberparm_improper_to_lt.py @@ -0,0 +1,62 @@ +#!/usr/bin/env python + +import sys + +lines_gaff = sys.stdin.readlines() +improper_style_name = 'cvff' + +sys.stdout.write(' write_once("In Settings") {\n') + +for i in range(0, len(lines_gaff)): + line = lines_gaff[i] + atypes = line[:11].split('-') + atype1 = atypes[0].strip() + atype2 = atypes[1].strip() + atype3 = atypes[2].strip() + atype4 = atypes[3].strip() + at1 = atype1.replace('X','*') + at2 = atype2.replace('X','*') + at3 = atype3.replace('X','*') + at4 = atype4.replace('X','*') + impropertype = '@improper:'+atype1+'-'+atype2+'-'+atype3+'-'+atype4 + + tokens= line[11:].split() + Kn = float(tokens[0]) + dn = float(tokens[1]) + n = int(float(tokens[2])) + comments=' '.join(tokens[3:]) + + if (dn < 0.001): + sys.stdout.write(' improper_coeff '+impropertype+' '+improper_style_name+' '+str(Kn)+' 1 '+str(n)+' # '+comments+'\n') + elif (179.999 < abs(dn) < 180.001): + sys.stdout.write(' improper_coeff '+impropertype+' '+improper_style_name+' '+str(Kn)+' -1 '+str(n)+' # '+comments+'\n') + else: + sys.stderr.write('Error: Illegal bondImproper parameters:\n' + ' As of 2013-8-03, LAMMPS doens hot have an improper style\n' + ' which can handle impropers with gamma != 0 or 180\n') + exit(-1) + + + +sys.stdout.write(' } # (end of improper_coeffs)\n') +sys.stdout.write('\n') +sys.stdout.write(' write_once("Data Impropers By Type") {\n') + +for i in range(0, len(lines_gaff)): + line = lines_gaff[i] + atypes = line[:11].split('-') + atype1 = atypes[0].strip() + atype2 = atypes[1].strip() + atype3 = atypes[2].strip() + atype4 = atypes[3].strip() + at1 = atype1.replace('X','*') + at2 = atype2.replace('X','*') + at3 = atype3.replace('X','*') + at4 = atype4.replace('X','*') + impropertype = '@improper:'+atype1+'-'+atype2+'-'+atype3+'-'+atype4 + + sys.stdout.write(' '+impropertype+' @atom:'+at1+' @atom:'+at2+' @atom:'+at3+' @atom:'+at4+'\n') + +sys.stdout.write(' } # (end of Impropers By Type)\n') +sys.stdout.write('\n') + diff --git a/tools/moltemplate/common/amber/amberparm_mass_to_lt.py b/tools/moltemplate/common/amber/amberparm_mass_to_lt.py new file mode 100755 index 000000000..818b1fa30 --- /dev/null +++ b/tools/moltemplate/common/amber/amberparm_mass_to_lt.py @@ -0,0 +1,19 @@ +#!/usr/bin/env python + +import sys + +lines_gaff = sys.stdin.readlines() + +sys.stdout.write(' write_once(\"Data Masses\") {\n') + +for i in range(0, len(lines_gaff)): + line = lines_gaff[i] + tokens= line.split() + atype = tokens[0] + mass=tokens[1] + # what is the next number? (the one in tokens[2]?) + comments=' '.join(tokens[3:]) + sys.stdout.write(' @atom:'+atype+' '+mass+' # '+comments+'\n') + +sys.stdout.write(' } # (end of masses)\n') +sys.stdout.write('\n') diff --git a/tools/moltemplate/common/amber/amberparm_pair_to_lt.py b/tools/moltemplate/common/amber/amberparm_pair_to_lt.py new file mode 100755 index 000000000..3bb9ddea5 --- /dev/null +++ b/tools/moltemplate/common/amber/amberparm_pair_to_lt.py @@ -0,0 +1,31 @@ +#!/usr/bin/env python + +import sys + +lines_gaff = sys.stdin.readlines() + +#pair_style = 'lj/charmm/coul/long' + + # NOTE: Long-range coulombic forces were disabled intentionally. (See below) + # If you want to use long-range electrostatics, uncomment these lines: + # Instead I use hybrid lj/charmm/coul/charmm by default, because + # LAMMPS complains if you attempt to use lj/charmm/coul/long on a + # system if it does not contain any charged particles. + # Currently, moltemplate does not assign atomic charge, + # so this problem occurs frequently. + +pair_style = 'lj/charmm/coul/charmm' + +sys.stdout.write(' write_once(\"In Settings\") {\n') + +for i in range(0, len(lines_gaff)): + line = lines_gaff[i] + tokens= line.split() + atype = tokens[0] + sig=tokens[1] + eps=tokens[2] + comments=' '.join(tokens[3:]) + sys.stdout.write(' pair_coeff @atom:'+atype+' @atom:'+atype+' '+pair_style+' '+eps+' '+sig+' # '+comments+'\n') + +sys.stdout.write(' } # (end of pair_coeffs)\n') +sys.stdout.write('\n') diff --git a/tools/moltemplate/common/gaff.lt b/tools/moltemplate/common/gaff.lt new file mode 100644 index 000000000..16d002081 --- /dev/null +++ b/tools/moltemplate/common/gaff.lt @@ -0,0 +1,11393 @@ +# This is the January 2013 version of GAFF (from AmberTools13). +#################################################################### +# To use this, LAMMPS currently must be compiled with the USER-MISC package. +# (Type "make yes-user-misc" into the shell before compiling LAMMPS.) +#################################################################### +# This moltemplate (LT) file was generated automatically using +# amberparm2lt.sh gaff.dat GAFF +#################################################################### +# Background information and usage explanation: +# This file contanis a list of atom types and rules for generating bonded +# interactions between these atoms (hopefully) according to AMBER conventions. +# By using the atom types shown below in your own molecules, bonds and angular +# interactions will be automatically generated. +# AMBER (GAFF) force-field parameters will also be assigned to each angle +# interaction (according to these atom types). +# One way to apply the GAFF force field to a particular type of molecule, is +# to use the "inherits" keyword when you define that molecule. For example: +# import("gaff.lt") +# MoleculeType inherits GAFF { +# write_once("Data Atoms") { +# $atom:C1 $mol:... @atom:cx 0.0 4.183 3.194 13.285 +# $atom:C2 $mol:... @atom:cx 0.0 4.291 4.618 13.382 +# : : : +# } +# } +#(See "Inheritance" and "short names vs. full names" in the moltemplate manual.) +#################################################################### +# Moltemplate can not assign atom charge. You must assign atomic +# charges yourself. (Moltemplate is only a simple text manipulation tool.) +#################################################################### + + +GAFF { + + # ---------------------------------------------------------------------- + # The basic atom nomenclature and conventions are explained here: + # http://ambermd.org/antechamber/gaff.pdf + # For reference, the original gaff.dat file and format documenation are here: + # http://ambermd.org/AmberTools-get.html + # http://ambermd.org/formats.html#parm.dat + # ---------------------------------------------------------------------- + + write_once("Data Masses") { + @atom:c 12.01 # Sp2 C carbonyl group + @atom:c1 12.01 # Sp C + @atom:c2 12.01 # Sp2 C + @atom:c3 12.01 # Sp3 C + @atom:ca 12.01 # Sp2 C in pure aromatic systems + @atom:cp 12.01 # Head Sp2 C that connect two rings in biphenyl sys. + @atom:cq 12.01 # Head Sp2 C that connect two rings in biphenyl sys. identical to cp + @atom:cc 12.01 # Sp2 carbons in non-pure aromatic systems + @atom:cd 12.01 # Sp2 carbons in non-pure aromatic systems, identical to cc + @atom:ce 12.01 # Inner Sp2 carbons in conjugated systems + @atom:cf 12.01 # Inner Sp2 carbons in conjugated systems, identical to ce + @atom:cg 12.01 # Inner Sp carbons in conjugated systems + @atom:ch 12.01 # Inner Sp carbons in conjugated systems, identical to cg + @atom:cx 12.01 # Sp3 carbons in triangle systems + @atom:cy 12.01 # Sp3 carbons in square systems + @atom:cu 12.01 # Sp2 carbons in triangle systems + @atom:cv 12.01 # Sp2 carbons in square systems + @atom:cz 12.01 # Sp2 carbon in guanidine group + @atom:h1 1.008 # H bonded to aliphatic carbon with 1 electrwd. group + @atom:h2 1.008 # H bonded to aliphatic carbon with 2 electrwd. group + @atom:h3 1.008 # H bonded to aliphatic carbon with 3 electrwd. group + @atom:h4 1.008 # H bonded to non-sp3 carbon with 1 electrwd. group + @atom:h5 1.008 # H bonded to non-sp3 carbon with 2 electrwd. group + @atom:ha 1.008 # H bonded to aromatic carbon + @atom:hc 1.008 # H bonded to aliphatic carbon without electrwd. group + @atom:hn 1.008 # H bonded to nitrogen atoms + @atom:ho 1.008 # Hydroxyl group + @atom:hp 1.008 # H bonded to phosphate + @atom:hs 1.008 # Hydrogen bonded to sulphur + @atom:hw 1.008 # Hydrogen in water + @atom:hx 1.008 # H bonded to C next to positively charged group + @atom:f 19.00 # Fluorine + @atom:cl 35.45 # Chlorine + @atom:br 79.90 # Bromine + @atom:i 126.9 # Iodine + @atom:n 14.01 # Sp2 nitrogen in amide groups + @atom:n1 14.01 # Sp N + @atom:n2 14.01 # aliphatic Sp2 N with two connected atoms + @atom:n3 14.01 # Sp3 N with three connected atoms + @atom:n4 14.01 # Sp3 N with four connected atoms + @atom:na 14.01 # Sp2 N with three connected atoms + @atom:nb 14.01 # Sp2 N in pure aromatic systems + @atom:nc 14.01 # Sp2 N in non-pure aromatic systems + @atom:nd 14.01 # Sp2 N in non-pure aromatic systems, identical to nc + @atom:ne 14.01 # Inner Sp2 N in conjugated systems + @atom:nf 14.01 # Inner Sp2 N in conjugated systems, identical to ne + @atom:nh 14.01 # Amine N connected one or more aromatic rings + @atom:no 14.01 # Nitro N + @atom:o 16.00 # Oxygen with one connected atom + @atom:oh 16.00 # Oxygen in hydroxyl group + @atom:os 16.00 # Ether and ester oxygen + @atom:ow 16.00 # Oxygen in water + @atom:p2 30.97 # Phosphate with two connected atoms + @atom:p3 30.97 # Phosphate with three connected atoms, such as PH3 + @atom:p4 30.97 # Phosphate with three connected atoms, such as O=P(CH3)2 + @atom:p5 30.97 # Phosphate with four connected atoms, such as O=P(OH)3 + @atom:pb 30.97 # Sp2 P in pure aromatic systems + @atom:pc 30.97 # Sp2 P in non-pure aromatic systems + @atom:pd 30.97 # Sp2 P in non-pure aromatic systems, identical to pc + @atom:pe 30.97 # Inner Sp2 P in conjugated systems + @atom:pf 30.97 # Inner Sp2 P in conjugated systems, identical to pe + @atom:px 30.97 # Special p4 in conjugated systems + @atom:py 30.97 # Special p5 in conjugated systems + @atom:s 32.06 # S with one connected atom + @atom:s2 32.06 # S with two connected atom, involved at least one double bond + @atom:s4 32.06 # S with three connected atoms + @atom:s6 32.06 # S with four connected atoms + @atom:sh 32.06 # Sp3 S connected with hydrogen + @atom:ss 32.06 # Sp3 S in thio-ester and thio-ether + @atom:sx 32.06 # Special s4 in conjugated systems + @atom:sy 32.06 # Special s6 in conjugated systems + } # (end of masses) + + write_once("In Settings") { + pair_coeff @atom:h1 @atom:h1 lj/charmm/coul/charmm 0.0157 1.3870 # Veenstra et al JCC,8,(1992),963 + pair_coeff @atom:h2 @atom:h2 lj/charmm/coul/charmm 0.0157 1.2870 # Veenstra et al JCC,8,(1992),963 + pair_coeff @atom:h3 @atom:h3 lj/charmm/coul/charmm 0.0157 1.1870 # Veenstra et al JCC,8,(1992),963 + pair_coeff @atom:h4 @atom:h4 lj/charmm/coul/charmm 0.0150 1.4090 # Spellmeyer, one electrowithdr. neighbor + pair_coeff @atom:h5 @atom:h5 lj/charmm/coul/charmm 0.0150 1.3590 # Spellmeyer, two electrowithdr. neighbor + pair_coeff @atom:ha @atom:ha lj/charmm/coul/charmm 0.0150 1.4590 # Spellmeyer + pair_coeff @atom:hc @atom:hc lj/charmm/coul/charmm 0.0157 1.4870 # OPLS + pair_coeff @atom:hn @atom:hn lj/charmm/coul/charmm 0.0157 0.6000 # !Ferguson base pair geom. + pair_coeff @atom:ho @atom:ho lj/charmm/coul/charmm 0.0000 0.0000 # OPLS Jorgensen, JACS,110,(1988),1657 + pair_coeff @atom:hp @atom:hp lj/charmm/coul/charmm 0.0157 0.6000 # same to hs (be careful !) + pair_coeff @atom:hs @atom:hs lj/charmm/coul/charmm 0.0157 0.6000 # W. Cornell CH3SH --> CH3OH FEP + pair_coeff @atom:hw @atom:hw lj/charmm/coul/charmm 0.0000 0.0000 # OPLS Jorgensen, JACS,110,(1988),1657 + pair_coeff @atom:hx @atom:hx lj/charmm/coul/charmm 0.0157 1.1000 # Veenstra et al JCC,8,(1992),963 + pair_coeff @atom:o @atom:o lj/charmm/coul/charmm 0.2100 1.6612 # OPLS + pair_coeff @atom:oh @atom:oh lj/charmm/coul/charmm 0.2104 1.7210 # OPLS + pair_coeff @atom:os @atom:os lj/charmm/coul/charmm 0.1700 1.6837 # OPLS ether + pair_coeff @atom:ow @atom:ow lj/charmm/coul/charmm 0.1520 1.7683 # TIP3P water model + pair_coeff @atom:c @atom:c lj/charmm/coul/charmm 0.0860 1.9080 # OPLS + pair_coeff @atom:c1 @atom:c1 lj/charmm/coul/charmm 0.2100 1.9080 # cp C DLM 11/2007 well depth from OPLS replacing 0.0860 + pair_coeff @atom:c2 @atom:c2 lj/charmm/coul/charmm 0.0860 1.9080 # sp2 atom in the middle of C=CD-CD=C + pair_coeff @atom:c3 @atom:c3 lj/charmm/coul/charmm 0.1094 1.9080 # OPLS + pair_coeff @atom:ca @atom:ca lj/charmm/coul/charmm 0.0860 1.9080 # OPLS + pair_coeff @atom:cc @atom:cc lj/charmm/coul/charmm 0.0860 1.9080 # OPLS + pair_coeff @atom:cd @atom:cd lj/charmm/coul/charmm 0.0860 1.9080 # OPLS + pair_coeff @atom:ce @atom:ce lj/charmm/coul/charmm 0.0860 1.9080 # OPLS + pair_coeff @atom:cf @atom:cf lj/charmm/coul/charmm 0.0860 1.9080 # OPLS + pair_coeff @atom:cg @atom:cg lj/charmm/coul/charmm 0.2100 1.9080 # DLM 12/2007 as c1 + pair_coeff @atom:ch @atom:ch lj/charmm/coul/charmm 0.2100 1.9080 # DLM 12/2007 as c1 + pair_coeff @atom:cp @atom:cp lj/charmm/coul/charmm 0.0860 1.9080 # OPLS + pair_coeff @atom:cq @atom:cq lj/charmm/coul/charmm 0.0860 1.9080 # OPLS + pair_coeff @atom:cu @atom:cu lj/charmm/coul/charmm 0.0860 1.9080 # OPLS + pair_coeff @atom:cv @atom:cv lj/charmm/coul/charmm 0.0860 1.9080 # OPLS + pair_coeff @atom:cx @atom:cx lj/charmm/coul/charmm 0.0860 1.9080 # OPLS + pair_coeff @atom:cy @atom:cy lj/charmm/coul/charmm 0.0860 1.9080 # OPLS + pair_coeff @atom:cz @atom:cz lj/charmm/coul/charmm 0.0860 1.9080 # OPLS + pair_coeff @atom:n @atom:n lj/charmm/coul/charmm 0.1700 1.8240 # OPLS + pair_coeff @atom:n1 @atom:n1 lj/charmm/coul/charmm 0.1700 1.8240 # OPLS + pair_coeff @atom:n2 @atom:n2 lj/charmm/coul/charmm 0.1700 1.8240 # OPLS + pair_coeff @atom:n3 @atom:n3 lj/charmm/coul/charmm 0.1700 1.8240 # OPLS + pair_coeff @atom:n4 @atom:n4 lj/charmm/coul/charmm 0.1700 1.8240 # OPLS + pair_coeff @atom:na @atom:na lj/charmm/coul/charmm 0.1700 1.8240 # OPLS + pair_coeff @atom:nb @atom:nb lj/charmm/coul/charmm 0.1700 1.8240 # OPLS + pair_coeff @atom:nc @atom:nc lj/charmm/coul/charmm 0.1700 1.8240 # OPLS + pair_coeff @atom:nd @atom:nd lj/charmm/coul/charmm 0.1700 1.8240 # OPLS + pair_coeff @atom:ne @atom:ne lj/charmm/coul/charmm 0.1700 1.8240 # OPLS + pair_coeff @atom:nf @atom:nf lj/charmm/coul/charmm 0.1700 1.8240 # OPLS + pair_coeff @atom:nh @atom:nh lj/charmm/coul/charmm 0.1700 1.8240 # OPLS + pair_coeff @atom:no @atom:no lj/charmm/coul/charmm 0.1700 1.8240 # OPLS + pair_coeff @atom:s @atom:s lj/charmm/coul/charmm 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's + pair_coeff @atom:s2 @atom:s2 lj/charmm/coul/charmm 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's + pair_coeff @atom:s4 @atom:s4 lj/charmm/coul/charmm 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's + pair_coeff @atom:s6 @atom:s6 lj/charmm/coul/charmm 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's + pair_coeff @atom:sx @atom:sx lj/charmm/coul/charmm 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's + pair_coeff @atom:sy @atom:sy lj/charmm/coul/charmm 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's + pair_coeff @atom:sh @atom:sh lj/charmm/coul/charmm 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's + pair_coeff @atom:ss @atom:ss lj/charmm/coul/charmm 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's + pair_coeff @atom:p2 @atom:p2 lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:p3 @atom:p3 lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:p4 @atom:p4 lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:p5 @atom:p5 lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:pb @atom:pb lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:pc @atom:pc lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:pd @atom:pd lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:pe @atom:pe lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:pf @atom:pf lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:px @atom:px lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:py @atom:py lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:f @atom:f lj/charmm/coul/charmm 0.061 1.75 # Gough et al. JCC 13,(1992),963. + pair_coeff @atom:cl @atom:cl lj/charmm/coul/charmm 0.265 1.948 # Fox, JPCB,102,8070,(98),flex.mdl CHCl3 + pair_coeff @atom:br @atom:br lj/charmm/coul/charmm 0.420 2.02 # Junmei, 2010 + pair_coeff @atom:i @atom:i lj/charmm/coul/charmm 0.50 2.15 # Junmei, 2010 + } # (end of pair_coeffs) + + write_once("In Settings") { + bond_coeff @bond:ow-hw harmonic 553.0 0.9572 # TIP3P_Water 1 + bond_coeff @bond:br-br harmonic 123.2 2.5420 # SOURCE1 4 0.0000 + bond_coeff @bond:br-c1 harmonic 352.7 1.7870 # SOURCE2 4 0.0024 + bond_coeff @bond:br-c2 harmonic 278.7 1.8830 # SOURCE1 31 0.0000 + bond_coeff @bond:br-c harmonic 240.3 1.9460 # SOURCE2 2 0.0285 + bond_coeff @bond:br-c3 harmonic 229.5 1.9660 # SOURCE1 100 0.0000 + bond_coeff @bond:br-ca harmonic 269.6 1.8970 # SOURCE1 127 0.0058 + bond_coeff @bond:br-cc harmonic 277.6 1.8847 # SOURCE4 39 0.0068 + bond_coeff @bond:br-cx harmonic 261.4 1.9100 # SOURCE1 8 0.0000 + bond_coeff @bond:br-i harmonic 142.4 2.6710 # SOURCE1 2 0.0245 + bond_coeff @bond:br-n1 harmonic 330.4 1.8600 # SOUECE3 1 + bond_coeff @bond:br-n2 harmonic 219.0 2.0380 # SOURCE3 5 0.1082 + bond_coeff @bond:br-n harmonic 320.2 1.8730 # SOURCE3 4 0.0046 + bond_coeff @bond:br-n3 harmonic 265.9 1.9520 # SOURCE3 2 0.0000 + bond_coeff @bond:br-n4 harmonic 282.4 1.9260 # SOURCE3 3 0.0013 + bond_coeff @bond:br-na harmonic 237.3 2.0020 # SOURCE3 7 0.2156 + bond_coeff @bond:br-nh harmonic 270.9 1.9440 # SOURCE3 1 0.0000 + bond_coeff @bond:br-no harmonic 191.0 2.1010 # SOURCE3 1 0.0000 + bond_coeff @bond:br-o harmonic 278.9 1.8000 # SOUECE3 1 + bond_coeff @bond:br-oh harmonic 237.2 1.8660 # SOURCE3 1 0.0000 + bond_coeff @bond:br-os harmonic 225.6 1.8870 # SOURCE3 2 0.0000 + bond_coeff @bond:br-p2 harmonic 174.3 2.2100 # SOURCE3 9 0.0510 + bond_coeff @bond:br-p3 harmonic 167.0 2.2310 # SOURCE3 3 0.0101 + bond_coeff @bond:br-p4 harmonic 188.8 2.1710 # SOUECE3 1 + bond_coeff @bond:br-p5 harmonic 179.3 2.1960 # SOURCE3 3 0.0099 + bond_coeff @bond:br-s harmonic 170.6 2.2200 # SOUECE3 1 + bond_coeff @bond:br-s4 harmonic 134.3 2.3410 # SOURCE3 1 0.0000 + bond_coeff @bond:br-s6 harmonic 172.7 2.2140 # SOURCE3 3 0.0443 + bond_coeff @bond:br-sh harmonic 174.4 2.2090 # SOURCE3 1 0.0000 + bond_coeff @bond:br-ss harmonic 176.6 2.2030 # SOURCE3 3 0.0035 + bond_coeff @bond:c1-c1 harmonic 986.2 1.1810 # SOURCE1 265 0.0031 + bond_coeff @bond:c1-c2 harmonic 625.0 1.3070 # SOURCE1 18 0.0000 + bond_coeff @bond:c1-c3 harmonic 368.3 1.4700 # SOURCE1 215 0.0017 + bond_coeff @bond:c1-ca harmonic 404.1 1.4400 # SOUECE3 1 + bond_coeff @bond:c1-ce harmonic 607.4 1.3153 # SOURCE4 6 0.0086 + bond_coeff @bond:c1-cg harmonic 845.8 1.2220 # SOURCE3 22 0.0101 + bond_coeff @bond:c1-ch harmonic 845.8 1.2220 # SOURCE3 22 same_as_c1-cg + bond_coeff @bond:c1-cl harmonic 419.7 1.6310 # SOURCE2 6 0.0050 + bond_coeff @bond:c1-cx harmonic 399.1 1.4440 # SOURCE1 38 0.0000 + bond_coeff @bond:c1-f harmonic 469.4 1.2700 # SOURCE2 2 0.0085 + bond_coeff @bond:c1-ha harmonic 375.9 1.0660 # SOURCE3 63 0.0035 + bond_coeff @bond:c1-hc harmonic 385.6 1.0600 # SOUECE3 1 + bond_coeff @bond:c1-i harmonic 318.8 1.9890 # SOURCE2 4 0.0032 + bond_coeff @bond:c1-n1 harmonic 1014.5 1.1380 # SOURCE1 170 0.0055 + bond_coeff @bond:c1-n2 harmonic 769.8 1.2100 # SOURCE3 5 0.0115 + bond_coeff @bond:c1-n3 harmonic 409.8 1.3920 # SOURCE2 1 0.0000 + bond_coeff @bond:c1-n4 harmonic 378.2 1.4170 # SOURCE3 3 0.0032 + bond_coeff @bond:c1-n harmonic 503.0 1.3300 # SOUECE3 1 + bond_coeff @bond:c1-na harmonic 452.0 1.3620 # SOURCE3 8 0.0034 + bond_coeff @bond:c1-ne harmonic 803.3 1.1986 # SOURCE4 10 0.0088 + bond_coeff @bond:c1-nf harmonic 803.3 1.1986 # SOURCE4 10 same_as_c1-ne + bond_coeff @bond:c1-nh harmonic 485.0 1.3408 # SOURCE4 11 0.0037 + bond_coeff @bond:c1-no harmonic 393.0 1.4050 # SOURCE3 3 0.0005 + bond_coeff @bond:c1-o harmonic 777.0 1.1660 # SOURCE2 9 0.0052 + bond_coeff @bond:c1-oh harmonic 435.6 1.3260 # SOURCE3 1 0.0000 + bond_coeff @bond:c1-os harmonic 437.1 1.3250 # SOURCE3 3 0.0148 + bond_coeff @bond:c1-p2 harmonic 289.3 1.7700 # SOUECE3 1 + bond_coeff @bond:c1-p3 harmonic 275.1 1.7900 # SOUECE3 1 + bond_coeff @bond:c1-p4 harmonic 275.1 1.7900 # SOUECE3 1 + bond_coeff @bond:c1-p5 harmonic 302.2 1.7530 # SOURCE3 2 0.0000 + bond_coeff @bond:c1-s2 harmonic 410.0 1.5950 # SOURCE3 1 0.0000 + bond_coeff @bond:c1-s harmonic 371.8 1.6300 # SOURCE1 14 0.0000 + bond_coeff @bond:c1-s4 harmonic 272.9 1.7460 # SOURCE3 2 0.0000 + bond_coeff @bond:c1-s6 harmonic 290.4 1.7220 # SOURCE3 2 0.0000 + bond_coeff @bond:c1-sh harmonic 324.5 1.6800 # SOUECE3 1 + bond_coeff @bond:c1-ss harmonic 325.4 1.6790 # SOURCE1 10 0.0000 + bond_coeff @bond:c2-c2 harmonic 589.7 1.3240 # SOURCE1 974 0.0096 + bond_coeff @bond:c2-c3 harmonic 328.3 1.5080 # SOURCE1 2536 0.0021 + bond_coeff @bond:c2-ca harmonic 357.2 1.4800 # SOUECE3 1 + bond_coeff @bond:c2-cc harmonic 522.6 1.3600 # SOURCE1 771 0.0185 + bond_coeff @bond:c2-cd harmonic 522.6 1.3600 # SOURCE1 771 0.0185 + bond_coeff @bond:c2-ce harmonic 560.5 1.3390 # SOURCE3 62 0.0128 + bond_coeff @bond:c2-cf harmonic 560.5 1.3390 # SOURCE3 62 same_as_c2-ce + bond_coeff @bond:c2-cl harmonic 328.8 1.7220 # SOURCE1 163 0.0098 + bond_coeff @bond:c2-cu harmonic 573.9 1.3320 # SOURCE2 1 0.0000 + bond_coeff @bond:c2-cx harmonic 353.3 1.4836 # SOURCE4 26 0.0064 + bond_coeff @bond:c2-cy harmonic 331.7 1.5046 # SOURCE4 9 0.0053 + bond_coeff @bond:c2-f harmonic 368.7 1.3400 # SOURCE1 34 0.0000 + bond_coeff @bond:c2-h4 harmonic 348.6 1.0840 # SOURCE3 40 0.0058 + bond_coeff @bond:c2-h5 harmonic 338.0 1.0915 # SOURCE4 42 0.0017 + bond_coeff @bond:c2-ha harmonic 344.3 1.0870 # SOURCE3 797 0.0046 + bond_coeff @bond:c2-hc harmonic 344.3 1.0870 # SOURCE3 789 0.0046 + bond_coeff @bond:c2-hx harmonic 350.1 1.0830 # SOURCE3 3 0.0008 + bond_coeff @bond:c2-i harmonic 223.2 2.1530 # SOURCE3 2 0.0000 + bond_coeff @bond:c2-n1 harmonic 546.0 1.3060 # SOURCE3 4 0.0161 + bond_coeff @bond:c2-n2 harmonic 581.1 1.2880 # SOURCE1 103 0.0100 + bond_coeff @bond:c2-n3 harmonic 486.3 1.3400 # SOUECE3 1 + bond_coeff @bond:c2-n harmonic 390.5 1.4070 # SOURCE3 9 0.0124 + bond_coeff @bond:c2-n4 harmonic 309.1 1.4820 # SOURCE3 5 0.0064 + bond_coeff @bond:c2-na harmonic 411.1 1.3910 # SOURCE3 31 0.0289 + bond_coeff @bond:c2-nc harmonic 533.0 1.3130 # SOURCE1 99 0.0095 + bond_coeff @bond:c2-nd harmonic 533.0 1.3130 # SOURCE1 99 same_as_c2-nc + bond_coeff @bond:c2-ne harmonic 597.7 1.2800 # SOURCE3 37 0.0110 + bond_coeff @bond:c2-nf harmonic 597.7 1.2800 # SOURCE3 37 same_as_c2-ne + bond_coeff @bond:c2-nh harmonic 462.6 1.3550 # SOURCE3 38 0.0413 + bond_coeff @bond:c2-no harmonic 345.6 1.4457 # SOURCE4 7 0.0087 + bond_coeff @bond:c2-o harmonic 623.6 1.2244 # SOURCE4 15 0.0036 + bond_coeff @bond:c2-oh harmonic 425.4 1.3330 # SOURCE1 53 0.0000 + bond_coeff @bond:c2-os harmonic 392.6 1.3570 # SOURCE1 315 0.0097 + bond_coeff @bond:c2-p2 harmonic 375.9 1.6700 # SOURCE3 62 0.0147 + bond_coeff @bond:c2-p3 harmonic 246.6 1.8340 # SOURCE3 5 0.0042 + bond_coeff @bond:c2-p4 harmonic 254.0 1.8220 # SOUECE3 1 + bond_coeff @bond:c2-p5 harmonic 228.2 1.8658 # SOURCE4 5 0.0025 + bond_coeff @bond:c2-pe harmonic 355.3 1.6910 # SOURCE3 52 0.0542 + bond_coeff @bond:c2-pf harmonic 355.3 1.6910 # SOURCE3 52 same_as_c2-pe + bond_coeff @bond:c2-s2 harmonic 393.1 1.6100 # SOURCE2 1 0.0000 + bond_coeff @bond:c2-s harmonic 281.5 1.7340 # SOURCE3 4 0.0034 + bond_coeff @bond:c2-s4 harmonic 263.2 1.7600 # SOUECE3 1 + bond_coeff @bond:c2-s6 harmonic 263.2 1.7600 # SOUECE3 1 + bond_coeff @bond:c2-sh harmonic 252.0 1.7771 # SOURCE4 5 0.0037 + bond_coeff @bond:c2-ss harmonic 280.0 1.7360 # SOURCE1 209 0.0155 + bond_coeff @bond:c3-c3 harmonic 303.1 1.5350 # SOURCE1 14664 0.0048 + bond_coeff @bond:c3-ca harmonic 323.5 1.5130 # SOURCE1 1813 0.0000 + bond_coeff @bond:c3-cc harmonic 337.3 1.4990 # SOURCE3 50 0.0096 + bond_coeff @bond:c3-cd harmonic 337.3 1.4990 # SOURCE3 50 0.0096 + bond_coeff @bond:c3-ce harmonic 331.3 1.5050 # SOURCE3 9 0.0024 + bond_coeff @bond:c3-cf harmonic 331.3 1.5050 # SOURCE3 9 same_as_c3-ce + bond_coeff @bond:c3-cl harmonic 279.0 1.7860 # SOURCE1 267 0.0194 + bond_coeff @bond:c3-cu harmonic 359.4 1.4780 # SOURCE1 7 0.0000 + bond_coeff @bond:c3-cv harmonic 347.6 1.4890 # SOURCE1 11 0.0000 + bond_coeff @bond:c3-cx harmonic 322.5 1.5140 # SOURCE1 712 0.0045 + bond_coeff @bond:c3-cy harmonic 308.5 1.5290 # SOURCE1 376 0.0000 + bond_coeff @bond:c3-f harmonic 363.8 1.3440 # SOURCE1 617 0.0281 + bond_coeff @bond:c3-h1 harmonic 335.9 1.0930 # SOURCE3 2175 0.0082 + bond_coeff @bond:c3-h2 harmonic 326.4 1.1000 # SOURCE3 66 0.0280 + bond_coeff @bond:c3-h3 harmonic 333.4 1.0948 # SOURCE4 25 0.0026 + bond_coeff @bond:c3-hc harmonic 337.3 1.0920 # SOURCE3 2815 0.0059 + bond_coeff @bond:c3-hx harmonic 338.7 1.0910 # SOURCE3 146 0.0066 + bond_coeff @bond:c3-i harmonic 219.1 2.1620 # SOURCE1 15 0.0000 + bond_coeff @bond:c3-n1 harmonic 325.1 1.4700 # SOURCE3 0 + bond_coeff @bond:c3-n2 harmonic 313.8 1.4770 # SOURCE1 129 0.0138 + bond_coeff @bond:c3-n harmonic 330.6 1.4600 # SOURCE1 187 0.0079 + bond_coeff @bond:c3-n3 harmonic 320.6 1.4700 # SOURCE1 1678 0.0017 + bond_coeff @bond:c3-n4 harmonic 293.6 1.4990 # SOURCE1 1370 0.0000 + bond_coeff @bond:c3-na harmonic 334.7 1.4560 # SOURCE3 23 0.0119 + bond_coeff @bond:c3-nc harmonic 334.7 1.4560 # SOURCE3 9 0.0109 + bond_coeff @bond:c3-nd harmonic 334.7 1.4560 # SOURCE3 9 same_as_c3-nc + bond_coeff @bond:c3-nh harmonic 332.7 1.4580 # SOURCE3 27 0.0085 + bond_coeff @bond:c3-no harmonic 265.4 1.5330 # SOURCE1 83 0.0212 + bond_coeff @bond:c3-o harmonic 449.9 1.3165 # SOURCE4 8 0.0193 + bond_coeff @bond:c3-oh harmonic 314.1 1.4260 # SOURCE1 914 0.0129 + bond_coeff @bond:c3-os harmonic 301.5 1.4390 # SOURCE1 3123 0.0126 + bond_coeff @bond:c3-p2 harmonic 234.3 1.8550 # SOURCE3 9 0.0125 + bond_coeff @bond:c3-p3 harmonic 240.6 1.8440 # SOURCE3 109 0.0107 + bond_coeff @bond:c3-p4 harmonic 247.2 1.8330 # SOURCE3 29 0.0138 + bond_coeff @bond:c3-p5 harmonic 259.7 1.8130 # SOURCE1 84 0.0000 + bond_coeff @bond:c3-px harmonic 252.7 1.8240 # SOURCE3 28 0.0098 + bond_coeff @bond:c3-py harmonic 259.7 1.8130 # SOURCE3 13 0.0163 + bond_coeff @bond:c3-s harmonic 212.9 1.8450 # SOURCE3 4 0.0185 + bond_coeff @bond:c3-s4 harmonic 233.8 1.8070 # SOURCE1 139 0.0023 + bond_coeff @bond:c3-s6 harmonic 254.0 1.7740 # SOURCE1 118 0.0103 + bond_coeff @bond:c3-sh harmonic 225.3 1.8220 # SOURCE3 12 0.0051 + bond_coeff @bond:c3-ss harmonic 225.8 1.8210 # SOURCE1 358 0.0075 + bond_coeff @bond:c3-sx harmonic 232.6 1.8090 # SOURCE3 30 0.0067 + bond_coeff @bond:c3-sy harmonic 248.9 1.7820 # SOURCE3 31 0.0039 + bond_coeff @bond:ca-ca harmonic 478.4 1.3870 # SOURCE1 6228 0.0147 + bond_coeff @bond:ca-cc harmonic 411.7 1.4340 # SOURCE1 80 0.0000 + bond_coeff @bond:ca-cd harmonic 411.7 1.4340 # SOURCE1 80 0.0000 + bond_coeff @bond:ca-ce harmonic 366.0 1.4720 # SOURCE1 71 0.0030 + bond_coeff @bond:ca-cf harmonic 366.0 1.4720 # SOURCE1 71 0.0030 + bond_coeff @bond:ca-cg harmonic 406.6 1.4380 # SOURCE1 71 0.0045 + bond_coeff @bond:ca-ch harmonic 406.6 1.4380 # SOURCE1 71 0.0045 + bond_coeff @bond:ca-cl harmonic 322.8 1.7290 # SOURCE1 704 0.0095 + bond_coeff @bond:ca-cp harmonic 466.1 1.3950 # SOURCE3 14 0.0110 + bond_coeff @bond:ca-cq harmonic 457.4 1.4009 # SOURCE4 14 0.0058 + bond_coeff @bond:ca-cx harmonic 350.8 1.4860 # SOURCE1 98 0.0118 + bond_coeff @bond:ca-cy harmonic 323.0 1.5135 # SOURCE4 8 0.0043 + bond_coeff @bond:ca-f harmonic 363.8 1.3440 # SOURCE1 205 0.0089 + bond_coeff @bond:ca-h4 harmonic 342.9 1.0880 # SOURCE3 57 0.0026 + bond_coeff @bond:ca-h5 harmonic 347.2 1.0850 # SOURCE3 15 0.0048 + bond_coeff @bond:ca-ha harmonic 344.3 1.0870 # SOURCE3 1496 0.0045 + bond_coeff @bond:ca-i harmonic 252.4 2.0950 # SOURCE1 51 0.0000 + bond_coeff @bond:ca-n1 harmonic 398.1 1.4000 # SOURCE3 0 + bond_coeff @bond:ca-n2 harmonic 551.6 1.3030 # SOURCE4 7 0.0058 + bond_coeff @bond:ca-n harmonic 372.3 1.4220 # SOURCE3 9 0.0098 + bond_coeff @bond:ca-n4 harmonic 325.6 1.4650 # SOURCE1 23 0.0000 + bond_coeff @bond:ca-na harmonic 470.3 1.3500 # SOURCE1 150 0.0103 + bond_coeff @bond:ca-nb harmonic 483.1 1.3420 # SOURCE3 104 0.0076 + bond_coeff @bond:ca-nc harmonic 492.9 1.3360 # SOURCE1 1826 0.0020 + bond_coeff @bond:ca-nd harmonic 492.9 1.3360 # SOURCE1 1826 0.0020 + bond_coeff @bond:ca-ne harmonic 361.8 1.4310 # SOURCE1 52 0.0000 + bond_coeff @bond:ca-nf harmonic 361.8 1.4310 # SOURCE1 52 0.0000 + bond_coeff @bond:ca-nh harmonic 449.0 1.3640 # SOURCE1 137 0.0085 + bond_coeff @bond:ca-no harmonic 322.6 1.4680 # SOURCE1 556 0.0000 + bond_coeff @bond:ca-o harmonic 610.0 1.2304 # SOURCE4 5 0.0026 + bond_coeff @bond:ca-oh harmonic 386.1 1.3620 # SOURCE1 551 0.0000 + bond_coeff @bond:ca-os harmonic 372.4 1.3730 # SOURCE1 1092 0.0071 + bond_coeff @bond:ca-p2 harmonic 243.0 1.8400 # SOUECE3 1 + bond_coeff @bond:ca-p3 harmonic 252.7 1.8240 # SOURCE1 145 0.0187 + bond_coeff @bond:ca-p4 harmonic 264.3 1.8060 # SOUECE3 1 + bond_coeff @bond:ca-p5 harmonic 271.6 1.7950 # SOURCE1 571 0.0028 + bond_coeff @bond:ca-pe harmonic 249.6 1.8290 # SOURCE3 10 0.0042 + bond_coeff @bond:ca-pf harmonic 249.6 1.8290 # SOURCE3 10 0.0042 + bond_coeff @bond:ca-px harmonic 252.1 1.8250 # SOURCE3 5 0.0168 + bond_coeff @bond:ca-py harmonic 268.3 1.7999 # SOURCE4 5 0.0072 + bond_coeff @bond:ca-s harmonic 277.9 1.7390 # SOURCE3 2 0.0000 + bond_coeff @bond:ca-s4 harmonic 245.2 1.7880 # SOURCE1 51 0.0048 + bond_coeff @bond:ca-s6 harmonic 263.9 1.7590 # SOURCE1 229 0.0036 + bond_coeff @bond:ca-sh harmonic 251.3 1.7783 # SOURCE4 12 0.0041 + bond_coeff @bond:ca-ss harmonic 256.6 1.7700 # SOURCE1 297 0.0041 + bond_coeff @bond:ca-sx harmonic 223.5 1.8252 # SOURCE4 24 0.0032 + bond_coeff @bond:ca-sy harmonic 247.7 1.7840 # SOURCE3 13 0.0094 + bond_coeff @bond:c-c1 harmonic 379.8 1.4600 # SOUECE3 1 + bond_coeff @bond:c-c2 harmonic 449.9 1.4060 # SOURCE3 2 0.0370 + bond_coeff @bond:c-c harmonic 290.1 1.5500 # SOURCE1 31 0.0100 + bond_coeff @bond:c-c3 harmonic 328.3 1.5080 # SOURCE1 2949 0.0060 + bond_coeff @bond:c-ca harmonic 349.7 1.4870 # SOURCE1 480 0.0055 + bond_coeff @bond:c-cc harmonic 377.4 1.4620 # SOURCE3 132 0.0210 + bond_coeff @bond:cc-cc harmonic 418.3 1.4290 # SOURCE1 740 0.0069 + bond_coeff @bond:cc-cd harmonic 504.0 1.3710 # SOURCE3 523 0.0217 + bond_coeff @bond:cc-ce harmonic 391.4 1.4502 # SOURCE4 157 0.0098 + bond_coeff @bond:cc-cf harmonic 521.7 1.3605 # SOURCE4 27 0.0086 + bond_coeff @bond:cc-cg harmonic 420.9 1.4270 # SOURCE1 560 0.0000 + bond_coeff @bond:cc-ch harmonic 420.9 1.4270 # SOURCE1 560 0.0000 + bond_coeff @bond:cc-cl harmonic 317.1 1.7359 # SOURCE4 55 0.0078 + bond_coeff @bond:cc-cx harmonic 369.3 1.4691 # SOURCE4 18 0.0037 + bond_coeff @bond:c-cd harmonic 377.4 1.4620 # SOURCE3 132 0.0210 + bond_coeff @bond:c-ce harmonic 363.8 1.4740 # SOURCE1 601 0.0105 + bond_coeff @bond:c-cf harmonic 363.8 1.4740 # SOURCE1 601 0.0105 + bond_coeff @bond:cc-f harmonic 368.6 1.3401 # SOURCE4 24 0.0034 + bond_coeff @bond:c-cg harmonic 389.3 1.4520 # SOURCE3 2 0.0000 + bond_coeff @bond:c-ch harmonic 389.3 1.4520 # SOURCE3 2 same_as_c-cg + bond_coeff @bond:cc-h4 harmonic 350.1 1.0830 # SOURCE3 599 0.0037 + bond_coeff @bond:cc-h5 harmonic 356.0 1.0790 # SOURCE3 40 0.0051 + bond_coeff @bond:cc-ha harmonic 347.2 1.0850 # SOURCE3 740 0.0039 + bond_coeff @bond:c-cl harmonic 293.5 1.7660 # SOURCE3 6 0.0250 + bond_coeff @bond:cc-n2 harmonic 572.5 1.2923 # SOURCE4 61 0.0067 + bond_coeff @bond:cc-n harmonic 426.0 1.3800 # SOURCE3 56 0.0109 + bond_coeff @bond:cc-n4 harmonic 299.0 1.4930 # SOURCE4 7 0.0148 + bond_coeff @bond:cc-na harmonic 438.8 1.3710 # SOURCE3 440 0.0144 + bond_coeff @bond:cc-nc harmonic 431.6 1.3760 # SOURCE1 88 0.0000 + bond_coeff @bond:cc-nd harmonic 494.6 1.3350 # SOURCE3 203 0.0239 + bond_coeff @bond:cc-ne harmonic 427.4 1.3790 # SOURCE4 30 0.0126 + bond_coeff @bond:cc-nf harmonic 580.1 1.2885 # SOURCE4 10 0.0112 + bond_coeff @bond:cc-nh harmonic 449.0 1.3640 # SOURCE3 6 0.0040 + bond_coeff @bond:cc-no harmonic 367.4 1.4262 # SOURCE4 133 0.0061 + bond_coeff @bond:cc-oh harmonic 411.8 1.3427 # SOURCE4 64 0.0073 + bond_coeff @bond:cc-os harmonic 376.1 1.3700 # SOURCE3 86 0.0192 + bond_coeff @bond:cc-pd harmonic 318.2 1.7330 # SOURCE3 84 0.0161 + bond_coeff @bond:cc-sh harmonic 257.9 1.7681 # SOURCE4 8 0.0027 + bond_coeff @bond:cc-ss harmonic 279.3 1.7370 # SOURCE3 52 0.0194 + bond_coeff @bond:cc-sx harmonic 231.3 1.8113 # SOURCE4 16 0.0050 + bond_coeff @bond:cc-sy harmonic 245.7 1.7872 # SOURCE4 33 0.0105 + bond_coeff @bond:c-cu harmonic 441.4 1.4120 # SOURCE2 1 0.0000 + bond_coeff @bond:c-cx harmonic 350.8 1.4860 # SOURCE1 105 0.0000 + bond_coeff @bond:c-cy harmonic 308.5 1.5290 # SOURCE1 18 0.0000 + bond_coeff @bond:cd-cd harmonic 418.3 1.4290 # SOURCE1 740 0.0069 + bond_coeff @bond:cd-ce harmonic 504.8 1.3705 # SOURCE4 43 0.0138 + bond_coeff @bond:cd-cf harmonic 381.8 1.4583 # SOURCE4 92 0.0079 + bond_coeff @bond:cd-cg harmonic 420.9 1.4270 # SOURCE1 560 0.0000 + bond_coeff @bond:cd-ch harmonic 420.9 1.4270 # SOURCE1 560 0.0000 + bond_coeff @bond:cd-cl harmonic 317.3 1.7356 # SOURCE4 11 0.0080 + bond_coeff @bond:cd-cx harmonic 358.6 1.4787 # SOURCE4 6 0.0029 + bond_coeff @bond:cd-cy harmonic 330.9 1.5054 # SOURCE4 10 0.0008 + bond_coeff @bond:cd-h4 harmonic 350.1 1.0830 # SOURCE3 599 0.0037 + bond_coeff @bond:cd-h5 harmonic 356.0 1.0790 # SOURCE3 40 0.0051 + bond_coeff @bond:cd-ha harmonic 347.2 1.0850 # SOURCE3 740 0.0039 + bond_coeff @bond:cd-n2 harmonic 577.7 1.2897 # SOURCE4 20 0.0086 + bond_coeff @bond:cd-n harmonic 426.0 1.3800 # SOURCE3 56 0.0109 + bond_coeff @bond:cd-na harmonic 438.8 1.3710 # SOURCE3 440 0.0144 + bond_coeff @bond:cd-nc harmonic 494.6 1.3350 # SOURCE3 203 0.0239 + bond_coeff @bond:cd-nd harmonic 431.6 1.3760 # SOURCE1 88 0.0000 + bond_coeff @bond:cd-ne harmonic 554.1 1.3017 # SOURCE4 13 0.0118 + bond_coeff @bond:cd-nh harmonic 449.0 1.3640 # SOURCE3 6 0.0040 + bond_coeff @bond:cd-oh harmonic 404.7 1.3479 # SOURCE4 57 0.0063 + bond_coeff @bond:cd-os harmonic 376.1 1.3700 # SOURCE3 86 0.0192 + bond_coeff @bond:cd-pc harmonic 318.2 1.7330 # SOURCE3 84 same_as_cc-pd + bond_coeff @bond:cd-ss harmonic 279.3 1.7370 # SOURCE3 52 0.0194 + bond_coeff @bond:cd-sy harmonic 251.7 1.7777 # SOURCE4 22 0.0034 + bond_coeff @bond:ce-ce harmonic 390.5 1.4510 # SOURCE1 66 0.0060 + bond_coeff @bond:ce-cf harmonic 562.4 1.3380 # SOURCE1 543 0.0045 + bond_coeff @bond:ce-cg harmonic 415.6 1.4310 # SOURCE1 22 0.0000 + bond_coeff @bond:ce-ch harmonic 415.6 1.4310 # SOURCE1 22 0.0000 + bond_coeff @bond:ce-cl harmonic 292.6 1.7671 # SOURCE4 24 0.0062 + bond_coeff @bond:ce-cx harmonic 337.0 1.4993 # SOURCE4 5 0.0066 + bond_coeff @bond:ce-cy harmonic 323.0 1.5135 # SOURCE4 17 0.0024 + bond_coeff @bond:ce-h4 harmonic 337.8 1.0916 # SOURCE4 125 0.0033 + bond_coeff @bond:ce-ha harmonic 341.5 1.0890 # SOURCE3 55 0.0056 + bond_coeff @bond:ce-n1 harmonic 540.3 1.3090 # SOURCE4 10 0.0027 + bond_coeff @bond:ce-n2 harmonic 599.8 1.2790 # SOURCE1 75 0.0000 + bond_coeff @bond:ce-n harmonic 369.2 1.4246 # SOURCE4 130 0.0066 + bond_coeff @bond:ce-na harmonic 373.8 1.4207 # SOURCE4 5 0.0051 + bond_coeff @bond:ce-ne harmonic 381.8 1.4140 # SOURCE3 7 0.0103 + bond_coeff @bond:ce-nf harmonic 571.9 1.2926 # SOURCE4 15 0.0042 + bond_coeff @bond:ce-nh harmonic 410.8 1.3912 # SOURCE4 148 0.0104 + bond_coeff @bond:ce-oh harmonic 395.9 1.3545 # SOURCE4 23 0.0100 + bond_coeff @bond:ce-os harmonic 370.6 1.3745 # SOURCE4 39 0.0077 + bond_coeff @bond:ce-p2 harmonic 259.1 1.8140 # SOUECE3 1 + bond_coeff @bond:ce-pe harmonic 256.5 1.8180 # SOURCE3 8 0.0108 + bond_coeff @bond:ce-px harmonic 254.6 1.8210 # SOURCE3 6 0.0046 + bond_coeff @bond:ce-py harmonic 272.3 1.7940 # SOURCE3 5 0.0045 + bond_coeff @bond:ce-s harmonic 324.5 1.6800 # SOUECE3 1 + bond_coeff @bond:ce-ss harmonic 243.6 1.7906 # SOURCE4 10 0.0064 + bond_coeff @bond:ce-sx harmonic 239.7 1.7970 # SOURCE3 5 0.0082 + bond_coeff @bond:ce-sy harmonic 248.9 1.7820 # SOURCE3 5 0.0114 + bond_coeff @bond:c-f harmonic 387.9 1.3250 # SOURCE2 6 0.0147 + bond_coeff @bond:cf-cf harmonic 390.5 1.4510 # SOURCE1 66 0.0060 + bond_coeff @bond:cf-cg harmonic 415.6 1.4310 # SOURCE1 22 0.0000 + bond_coeff @bond:cf-ch harmonic 415.6 1.4310 # SOURCE1 22 0.0000 + bond_coeff @bond:cf-h4 harmonic 334.5 1.0940 # SOURCE4 19 0.0019 + bond_coeff @bond:cf-ha harmonic 341.5 1.0890 # SOURCE3 55 0.0056 + bond_coeff @bond:cf-n1 harmonic 522.2 1.3190 # SOURCE3 3 0.0121 + bond_coeff @bond:cf-n2 harmonic 599.8 1.2790 # SOURCE1 75 same_as_ce-n2 + bond_coeff @bond:cf-n harmonic 362.6 1.4303 # SOURCE4 6 0.0082 + bond_coeff @bond:cf-ne harmonic 575.1 1.2910 # SOURCE4 27 0.0083 + bond_coeff @bond:cf-nf harmonic 381.8 1.4140 # SOURCE3 7 same_as_ce-ne + bond_coeff @bond:cf-nh harmonic 423.0 1.3822 # SOURCE4 20 0.0102 + bond_coeff @bond:cf-oh harmonic 414.4 1.3408 # SOURCE4 14 0.0084 + bond_coeff @bond:cf-os harmonic 387.2 1.3612 # SOURCE4 6 0.0111 + bond_coeff @bond:cf-p2 harmonic 259.1 1.8140 # SOUECE3 1 same_as_ce-p2 + bond_coeff @bond:cf-pf harmonic 256.5 1.8180 # SOURCE3 8 same_as_ce-pe + bond_coeff @bond:cf-px harmonic 254.6 1.8210 # SOURCE3 6 same_as_ce-px + bond_coeff @bond:cf-py harmonic 272.3 1.7940 # SOURCE3 5 same_as_ce-py + bond_coeff @bond:cf-s harmonic 324.5 1.6800 # SOUECE3 1 same_as_ce-s + bond_coeff @bond:cf-sx harmonic 239.7 1.7970 # SOURCE3 5 same_as_ce-sx + bond_coeff @bond:cf-sy harmonic 248.9 1.7820 # SOURCE3 5 same_as_ce-sy + bond_coeff @bond:cg-cg harmonic 494.2 1.3770 # SOURCE1 42 0.0000 + bond_coeff @bond:cg-ch harmonic 949.5 1.1910 # SOURCE1 80 0.0015 + bond_coeff @bond:cg-n1 harmonic 994.7 1.1430 # SOURCE1 316 0.0018 + bond_coeff @bond:cg-ne harmonic 509.5 1.3262 # SOURCE4 17 0.0009 + bond_coeff @bond:cg-pe harmonic 429.8 1.6210 # SOURCE3 11 0.2008 + bond_coeff @bond:c-h4 harmonic 310.5 1.1123 # SOURCE4 125 0.0023 + bond_coeff @bond:c-h5 harmonic 319.4 1.1053 # SOURCE4 42 0.0028 + bond_coeff @bond:c-ha harmonic 325.1 1.1010 # SOURCE3 53 0.0102 + bond_coeff @bond:ch-ch harmonic 494.2 1.3770 # SOURCE1 42 0.0000 + bond_coeff @bond:ch-n1 harmonic 994.7 1.1430 # SOURCE1 316 0.0018 + bond_coeff @bond:ch-nf harmonic 509.5 1.3262 # SOURCE4 17 same_as_cg-ne + bond_coeff @bond:ch-pf harmonic 429.8 1.6210 # SOURCE3 11 same_as_cg-pe + bond_coeff @bond:c-i harmonic 198.9 2.2090 # SOURCE3 4 0.0365 + bond_coeff @bond:cl-cl harmonic 143.3 2.2670 # SOURCE1 2 0.0395 + bond_coeff @bond:cl-cx harmonic 301.8 1.7550 # SOURCE1 64 0.0000 + bond_coeff @bond:cl-cy harmonic 292.0 1.7680 # SOURCE2 2 0.0070 + bond_coeff @bond:cl-f harmonic 298.6 1.6480 # SOURCE2 2 0.0500 + bond_coeff @bond:cl-i harmonic 163.5 2.5500 # SOURCE1 6 0.0893 + bond_coeff @bond:cl-n1 harmonic 431.6 1.6300 # SOUECE3 1 + bond_coeff @bond:cl-n2 harmonic 263.4 1.8190 # SOURCE3 6 0.1020 + bond_coeff @bond:cl-n3 harmonic 290.4 1.7800 # SOURCE4 5 0.0021 + bond_coeff @bond:cl-n harmonic 344.2 1.7140 # SOURCE4 5 0.0005 + bond_coeff @bond:cl-n4 harmonic 311.1 1.7530 # SOURCE3 4 0.0098 + bond_coeff @bond:cl-na harmonic 253.2 1.8350 # SOURCE3 7 0.2083 + bond_coeff @bond:cl-nh harmonic 303.2 1.7630 # SOURCE3 1 0.0000 + bond_coeff @bond:cl-no harmonic 250.1 1.8400 # SOURCE2 1 0.0000 + bond_coeff @bond:cl-o harmonic 557.6 1.4830 # SOURCE3 4 0.0000 + bond_coeff @bond:cl-oh harmonic 309.7 1.6900 # SOURCE2 1 0.0000 + bond_coeff @bond:cl-os harmonic 278.8 1.7300 # SOURCE3 4 0.0000 + bond_coeff @bond:cl-p2 harmonic 217.5 2.0700 # SOURCE3 6 0.0108 + bond_coeff @bond:cl-p3 harmonic 249.4 2.0080 # SOURCE1 111 0.0000 + bond_coeff @bond:cl-p4 harmonic 249.4 2.0080 # SOURCE1 111 0.0000 + bond_coeff @bond:cl-p5 harmonic 249.4 2.0080 # SOURCE1 111 0.0000 + bond_coeff @bond:cl-pb harmonic 255.6 1.9970 # SOURCE1 46 0.0000 + bond_coeff @bond:cl-s harmonic 208.7 2.0720 # SOURCE1 6 0.0000 + bond_coeff @bond:cl-s2 harmonic 172.7 2.1610 # SOURCE2 1 0.0000 + bond_coeff @bond:cl-s4 harmonic 208.7 2.0720 # SOURCE1 6 0.0000 + bond_coeff @bond:cl-s6 harmonic 208.7 2.0720 # SOURCE1 6 0.0000 + bond_coeff @bond:cl-sh harmonic 208.7 2.0720 # SOURCE1 6 0.0000 + bond_coeff @bond:cl-ss harmonic 208.7 2.0720 # SOURCE1 6 0.0000 + bond_coeff @bond:cl-sx harmonic 208.7 2.0720 # SOURCE1 6 0.0000 + bond_coeff @bond:cl-sy harmonic 208.7 2.0720 # SOURCE1 6 0.0000 + bond_coeff @bond:c-n2 harmonic 374.6 1.4200 # SOUECE3 1 + bond_coeff @bond:c-n4 harmonic 255.5 1.5460 # SOURCE3 4 0.0388 + bond_coeff @bond:c-n harmonic 478.2 1.3450 # SOURCE1 1235 0.0215 + bond_coeff @bond:c-nc harmonic 428.3 1.3784 # SOURCE4 70 0.0128 + bond_coeff @bond:c-nd harmonic 391.2 1.4064 # SOURCE4 54 0.0130 + bond_coeff @bond:c-ne harmonic 408.6 1.3929 # SOURCE4 47 0.0136 + bond_coeff @bond:c-nf harmonic 404.8 1.3958 # SOURCE4 5 0.0122 + bond_coeff @bond:c-no harmonic 260.1 1.5400 # SOUECE3 1 + bond_coeff @bond:c-o harmonic 648.0 1.2140 # SOURCE1 3682 0.0165 + bond_coeff @bond:c-oh harmonic 466.4 1.3060 # SOURCE1 271 0.0041 + bond_coeff @bond:c-os harmonic 411.3 1.3430 # SOURCE1 1044 0.0171 + bond_coeff @bond:c-p2 harmonic 210.3 1.9000 # SOUECE3 1 + bond_coeff @bond:c-p3 harmonic 219.0 1.8830 # SOURCE3 6 0.0129 + bond_coeff @bond:c-p4 harmonic 220.6 1.8800 # SOUECE3 1 + bond_coeff @bond:c-p5 harmonic 219.8 1.8815 # SOURCE4 11 0.0078 + bond_coeff @bond:cp-cp harmonic 346.5 1.4900 # SOURCE1 242 0.0010 + bond_coeff @bond:cp-cq harmonic 419.3 1.4282 # SOURCE4 7 0.0034 + bond_coeff @bond:c-pe harmonic 204.9 1.9110 # SOURCE3 3 0.0025 + bond_coeff @bond:c-pf harmonic 204.9 1.9110 # SOURCE3 3 same_as_c-pe + bond_coeff @bond:cp-na harmonic 420.5 1.3840 # SOURCE4 7 0.0181 + bond_coeff @bond:cp-nb harmonic 486.7 1.3398 # SOURCE4 70 0.0062 + bond_coeff @bond:c-px harmonic 208.3 1.9040 # SOURCE3 1 0.0000 + bond_coeff @bond:c-py harmonic 227.6 1.8670 # SOURCE3 6 0.0199 + bond_coeff @bond:cq-cq harmonic 346.5 1.4900 # SOURCE1 242 0.0010 + bond_coeff @bond:c-s harmonic 328.9 1.6750 # SOURCE1 401 0.0128 + bond_coeff @bond:c-s4 harmonic 200.4 1.8700 # SOUECE3 1 + bond_coeff @bond:c-s6 harmonic 200.4 1.8700 # SOUECE3 1 + bond_coeff @bond:c-sh harmonic 249.6 1.7810 # SOURCE3 6 0.0171 + bond_coeff @bond:c-ss harmonic 261.9 1.7620 # SOURCE1 20 0.0000 + bond_coeff @bond:c-sx harmonic 193.3 1.8850 # SOURCE3 5 0.0088 + bond_coeff @bond:c-sy harmonic 202.8 1.8650 # SOURCE3 5 0.0085 + bond_coeff @bond:cu-cu harmonic 653.7 1.2940 # SOURCE1 10 0.0000 + bond_coeff @bond:cu-cx harmonic 327.3 1.5090 # SOURCE1 20 0.0000 + bond_coeff @bond:cu-ha harmonic 353.0 1.0810 # SOURCE2 3 0.0111 + bond_coeff @bond:cv-cv harmonic 568.1 1.3350 # SOURCE1 25 0.0000 + bond_coeff @bond:cv-cy harmonic 323.5 1.5130 # SOURCE1 50 0.0000 + bond_coeff @bond:cv-ha harmonic 344.3 1.0870 # SOURCE3 2 0.0000 + bond_coeff @bond:cx-cv harmonic 328.3 1.5080 # SOURCE1 2536 as + bond_coeff @bond:cx-cx harmonic 337.3 1.4990 # SOURCE1 1204 0.0183 + bond_coeff @bond:cx-cy harmonic 321.5 1.5150 # SOURCE3 2 0.0000 + bond_coeff @bond:cx-f harmonic 347.2 1.3580 # SOURCE2 3 0.0050 + bond_coeff @bond:cx-h1 harmonic 344.3 1.0870 # SOURCE3 10 0.0017 + bond_coeff @bond:cx-h2 harmonic 350.1 1.0830 # SOURCE3 2 0.0000 + bond_coeff @bond:cx-hc harmonic 345.8 1.0860 # SOURCE3 44 0.0011 + bond_coeff @bond:cx-hx harmonic 347.2 1.0850 # SOURCE4 5 0.0002 + bond_coeff @bond:cx-n2 harmonic 309.1 1.4820 # SOURCE3 2 0.0000 + bond_coeff @bond:cx-n3 harmonic 318.7 1.4720 # SOURCE1 134 0.0000 + bond_coeff @bond:cx-n harmonic 350.6 1.4411 # SOURCE4 11 0.0092 + bond_coeff @bond:cx-na harmonic 329.0 1.4616 # SOURCE4 11 0.0016 + bond_coeff @bond:cx-nh harmonic 336.7 1.4541 # SOURCE4 83 0.0076 + bond_coeff @bond:cx-oh harmonic 387.4 1.3610 # SOURCE3 3 0.0018 + bond_coeff @bond:cx-os harmonic 320.1 1.4200 # SOURCE3 7 0.0222 + bond_coeff @bond:cx-p3 harmonic 227.6 1.8670 # SOURCE2 1 0.0000 + bond_coeff @bond:cx-s4 harmonic 225.3 1.8220 # SOURCE2 1 0.0000 + bond_coeff @bond:cx-s6 harmonic 283.7 1.7310 # SOURCE2 1 0.0000 + bond_coeff @bond:cx-ss harmonic 229.2 1.8150 # SOURCE2 1 0.0000 + bond_coeff @bond:cy-cy harmonic 286.8 1.5540 # SOURCE1 742 0.0041 + bond_coeff @bond:cy-f harmonic 355.5 1.3509 # SOURCE4 8 0.0047 + bond_coeff @bond:cy-h1 harmonic 330.4 1.0970 # SOURCE3 17 0.0058 + bond_coeff @bond:cy-h2 harmonic 335.8 1.0931 # SOURCE4 80 0.0019 + bond_coeff @bond:cy-hc harmonic 334.5 1.0940 # SOURCE3 63 0.0014 + bond_coeff @bond:cy-n harmonic 321.3 1.4693 # SOURCE4 250 0.0102 + bond_coeff @bond:cy-n3 harmonic 307.2 1.4840 # SOURCE1 21 0.0000 + bond_coeff @bond:cy-oh harmonic 325.2 1.4150 # SOURCE3 2 0.0000 + bond_coeff @bond:cy-os harmonic 308.6 1.4316 # SOURCE4 23 0.0136 + bond_coeff @bond:cy-s6 harmonic 209.6 1.8514 # SOURCE4 9 0.0166 + bond_coeff @bond:cy-ss harmonic 211.3 1.8481 # SOURCE4 78 0.0080 + bond_coeff @bond:cz-nh harmonic 487.8 1.3391 # SOURCE4 32 0.0045 + bond_coeff @bond:f-n1 harmonic 375.7 1.4100 # SOUECE3 1 + bond_coeff @bond:f-n2 harmonic 337.5 1.4440 # SOURCE3 5 0.0377 + bond_coeff @bond:f-n3 harmonic 380.6 1.4060 # SOURCE1 9 0.0000 + bond_coeff @bond:f-n harmonic 391.7 1.3970 # SOURCE3 3 0.0112 + bond_coeff @bond:f-n4 harmonic 526.8 1.3080 # SOURCE3 2 0.0000 + bond_coeff @bond:f-na harmonic 374.5 1.4110 # SOURCE3 7 0.0611 + bond_coeff @bond:f-nh harmonic 357.1 1.4260 # SOURCE3 3 0.0085 + bond_coeff @bond:f-no harmonic 314.4 1.4670 # SOURCE2 1 0.0000 + bond_coeff @bond:f-o harmonic 442.2 1.3300 # SOUECE3 1 + bond_coeff @bond:f-oh harmonic 305.4 1.4440 # SOURCE3 1 0.0000 + bond_coeff @bond:f-os harmonic 326.2 1.4230 # SOURCE3 2 0.0000 + bond_coeff @bond:f-p2 harmonic 287.3 1.5360 # SOURCE3 7 0.2054 + bond_coeff @bond:f-p3 harmonic 254.5 1.5780 # SOURCE2 8 0.0103 + bond_coeff @bond:f-p4 harmonic 246.0 1.5900 # SOUECE3 1 + bond_coeff @bond:f-p5 harmonic 253.8 1.5790 # SOURCE1 72 0.0000 + bond_coeff @bond:f-s2 harmonic 244.4 1.6430 # SOURCE2 1 0.0000 + bond_coeff @bond:f-s harmonic 233.3 1.6600 # SOUECE3 1 + bond_coeff @bond:f-s4 harmonic 282.4 1.5910 # SOURCE2 4 0.0065 + bond_coeff @bond:f-s6 harmonic 312.1 1.5560 # SOURCE2 5 0.0220 + bond_coeff @bond:f-sh harmonic 240.4 1.6490 # SOURCE3 1 0.0000 + bond_coeff @bond:f-ss harmonic 250.5 1.6340 # SOURCE3 3 0.0156 + bond_coeff @bond:hn-n1 harmonic 455.1 0.9860 # SOURCE2 1 0.0000 + bond_coeff @bond:hn-n2 harmonic 375.5 1.0290 # SOURCE3 108 0.0096 + bond_coeff @bond:hn-n3 harmonic 394.1 1.0180 # SOURCE3 157 0.0086 + bond_coeff @bond:hn-n harmonic 410.2 1.0090 # SOURCE3 149 0.0098 + bond_coeff @bond:hn-n4 harmonic 369.0 1.0330 # SOURCE3 264 0.0082 + bond_coeff @bond:hn-na harmonic 406.6 1.0110 # SOURCE3 46 0.0107 + bond_coeff @bond:hn-nh harmonic 401.2 1.0140 # SOURCE3 209 0.0091 + bond_coeff @bond:hn-no harmonic 385.6 1.0230 # SOURCE3 1 0.0000 + bond_coeff @bond:ho-o harmonic 357.9 0.9810 # SOURCE3 1 0.0000 + bond_coeff @bond:ho-oh harmonic 369.6 0.9740 # SOURCE3 367 0.0105 + bond_coeff @bond:hp-p2 harmonic 385.1 1.3360 # SOURCE3 87 0.1706 + bond_coeff @bond:hp-p3 harmonic 303.1 1.4090 # SOURCE3 101 0.0617 + bond_coeff @bond:hp-p4 harmonic 368.7 1.3490 # SOURCE3 17 0.1577 + bond_coeff @bond:hp-p5 harmonic 305.0 1.4070 # SOURCE3 7 0.0062 + bond_coeff @bond:hs-s harmonic 286.4 1.3530 # SOURCE3 1 0.0000 + bond_coeff @bond:hs-s4 harmonic 266.4 1.3750 # SOURCE3 5 0.0004 + bond_coeff @bond:hs-s6 harmonic 280.8 1.3590 # SOURCE3 5 0.0015 + bond_coeff @bond:hs-sh harmonic 302.2 1.3370 # SOURCE3 98 0.0486 + bond_coeff @bond:i-i harmonic 109.2 2.9170 # SOURCE1 1 0.0000 + bond_coeff @bond:i-n1 harmonic 302.1 2.0600 # SOUECE3 1 + bond_coeff @bond:i-n2 harmonic 182.6 2.3040 # SOURCE3 6 0.1186 + bond_coeff @bond:i-n harmonic 278.3 2.0980 # SOURCE3 5 0.0156 + bond_coeff @bond:i-n3 harmonic 231.8 2.1850 # SOURCE3 3 0.0437 + bond_coeff @bond:i-n4 harmonic 246.6 2.1550 # SOURCE3 3 0.0168 + bond_coeff @bond:i-na harmonic 260.5 2.1290 # SOURCE3 8 0.1276 + bond_coeff @bond:i-nh harmonic 249.2 2.1500 # SOURCE3 1 0.0000 + bond_coeff @bond:i-no harmonic 211.0 2.2310 # SOURCE3 1 0.0000 + bond_coeff @bond:i-o harmonic 323.8 1.9800 # SOUECE3 1 + bond_coeff @bond:i-oh harmonic 247.9 2.1010 # SOURCE3 2 0.0000 + bond_coeff @bond:i-os harmonic 233.6 2.1290 # SOURCE3 3 0.0146 + bond_coeff @bond:i-p2 harmonic 108.2 2.6430 # SOURCE3 6 0.0297 + bond_coeff @bond:i-p3 harmonic 123.6 2.5660 # SOURCE3 3 0.0016 + bond_coeff @bond:i-p4 harmonic 183.0 2.3520 # SOURCE3 4 0.2600 + bond_coeff @bond:i-p5 harmonic 117.3 2.5960 # SOURCE3 3 0.0143 + bond_coeff @bond:i-s harmonic 175.1 2.4300 # SOUECE3 1 + bond_coeff @bond:i-s4 harmonic 82.8 2.8700 # SOUECE3 1 + bond_coeff @bond:i-s6 harmonic 82.8 2.8700 # SOURCE3 1 0.0000 + bond_coeff @bond:i-sh harmonic 138.5 2.5600 # SOUECE3 1 + bond_coeff @bond:i-ss harmonic 135.9 2.5710 # SOURCE3 3 0.0065 + bond_coeff @bond:n1-n1 harmonic 1221.7 1.1240 # SOURCE1 19 0.0000 + bond_coeff @bond:n1-n2 harmonic 857.4 1.2160 # SOURCE1 19 0.0000 + bond_coeff @bond:n1-n3 harmonic 535.7 1.3500 # SOUECE3 1 + bond_coeff @bond:n1-n4 harmonic 518.2 1.3600 # SOUECE3 1 + bond_coeff @bond:n1-na harmonic 535.7 1.3500 # SOUECE3 1 + bond_coeff @bond:n1-nc harmonic 857.4 1.2160 # SOURCE1 38 0.0000 + bond_coeff @bond:n1-nd harmonic 857.4 1.2160 # SOURCE1 38 0.0000 + bond_coeff @bond:n1-ne harmonic 751.9 1.2520 # SOURCE2 1 0.0000 + bond_coeff @bond:n1-nf harmonic 751.9 1.2520 # SOURCE2 1 same_as_n1-ne + bond_coeff @bond:n1-nh harmonic 553.9 1.3400 # SOUECE3 1 + bond_coeff @bond:n1-no harmonic 454.8 1.4000 # SOUECE3 1 + bond_coeff @bond:n1-o harmonic 617.5 1.2770 # SOURCE3 5 0.0438 + bond_coeff @bond:n1-oh harmonic 569.8 1.3000 # SOUECE3 1 + bond_coeff @bond:n1-os harmonic 550.5 1.3100 # SOUECE3 1 + bond_coeff @bond:n1-p2 harmonic 358.8 1.6780 # SOURCE3 2 0.0282 + bond_coeff @bond:n1-p3 harmonic 376.7 1.6600 # SOUECE3 1 + bond_coeff @bond:n1-p4 harmonic 353.0 1.6800 # SOURCE3 0 + bond_coeff @bond:n1-p5 harmonic 482.7 1.5710 # SOURCE1 132 0.0000 + bond_coeff @bond:n1-s2 harmonic 604.3 1.4490 # SOURCE2 2 0.0010 + bond_coeff @bond:n1-s harmonic 328.7 1.6590 # SOURCE3 6 0.0789 + bond_coeff @bond:n1-s4 harmonic 336.8 1.6500 # SOUECE3 1 + bond_coeff @bond:n1-s6 harmonic 670.3 1.4160 # SOURCE2 2 0.0000 + bond_coeff @bond:n1-sh harmonic 376.1 1.6100 # SOUECE3 1 + bond_coeff @bond:n1-ss harmonic 376.1 1.6100 # SOUECE3 1 + bond_coeff @bond:n2-n2 harmonic 702.7 1.2710 # SOURCE3 27 0.0347 + bond_coeff @bond:n2-n3 harmonic 574.8 1.3290 # SOURCE2 1 0.0000 + bond_coeff @bond:n2-n4 harmonic 200.8 1.6790 # SOURCE3 7 0.3138 + bond_coeff @bond:n2-na harmonic 503.9 1.3685 # SOURCE4 18 0.0066 + bond_coeff @bond:n2-nc harmonic 743.9 1.2550 # SOURCE1 13 0.0000 + bond_coeff @bond:n2-nd harmonic 743.9 1.2550 # SOURCE1 13 same_as_n2_nc + bond_coeff @bond:n2-ne harmonic 685.5 1.2780 # SOURCE3 30 0.0302 + bond_coeff @bond:n2-nf harmonic 685.5 1.2780 # SOURCE3 30 same_as_n2-ne + bond_coeff @bond:n2-nh harmonic 525.1 1.3560 # SOURCE3 22 0.0300 + bond_coeff @bond:n2-no harmonic 231.9 1.6260 # SOURCE3 4 0.1933 + bond_coeff @bond:n2-o harmonic 789.9 1.2090 # SOURCE3 20 0.0344 + bond_coeff @bond:n2-oh harmonic 416.2 1.3940 # SOURCE1 67 0.0000 + bond_coeff @bond:n2-os harmonic 400.5 1.4060 # SOURCE3 10 0.0147 + bond_coeff @bond:n2-p2 harmonic 438.3 1.6050 # SOURCE3 35 0.0737 + bond_coeff @bond:n2-p3 harmonic 286.5 1.7640 # SOURCE3 7 0.0374 + bond_coeff @bond:n2-p4 harmonic 317.7 1.7240 # SOUECE3 1 + bond_coeff @bond:n2-p5 harmonic 445.8 1.5990 # SOURCE1 7 0.0000 + bond_coeff @bond:n2-pe harmonic 527.9 1.5400 # SOURCE3 20 0.1392 + bond_coeff @bond:n2-pf harmonic 527.9 1.5400 # SOURCE3 20 same_as_n2-pe + bond_coeff @bond:n2-s2 harmonic 499.0 1.5120 # SOURCE2 1 0.0000 + bond_coeff @bond:n2-s4 harmonic 376.1 1.6100 # SOUECE3 1 + bond_coeff @bond:n2-s harmonic 458.1 1.5410 # SOURCE1 37 0.0000 + bond_coeff @bond:n2-s6 harmonic 444.6 1.5513 # SOURCE4 5 0.0011 + bond_coeff @bond:n2-sh harmonic 266.6 1.7380 # SOURCE3 5 0.0511 + bond_coeff @bond:n2-ss harmonic 331.4 1.6560 # SOURCE1 36 0.0000 + bond_coeff @bond:n3-n3 harmonic 383.6 1.4540 # SOURCE1 44 0.0000 + bond_coeff @bond:n3-n4 harmonic 434.9 1.4140 # SOURCE1 13 0.0000 + bond_coeff @bond:n3-na harmonic 426.7 1.4200 # SOURCE1 68 0.0000 + bond_coeff @bond:n3-nh harmonic 426.7 1.4200 # SOURCE1 68 0.0000 + bond_coeff @bond:n3-no harmonic 394.5 1.4450 # SOURCE3 3 0.0208 + bond_coeff @bond:n3-o harmonic 564.0 1.3030 # SOURCE3 4 0.1217 + bond_coeff @bond:n3-oh harmonic 413.5 1.3960 # SOURCE1 28 0.0000 + bond_coeff @bond:n3-os harmonic 359.6 1.4400 # SOURCE1 34 0.0315 + bond_coeff @bond:n3-p2 harmonic 366.6 1.6700 # SOUECE3 1 + bond_coeff @bond:n3-p3 harmonic 312.8 1.7300 # SOURCE1 40 0.0000 + bond_coeff @bond:n3-p4 harmonic 341.1 1.6970 # SOURCE1 88 0.0000 + bond_coeff @bond:n3-p5 harmonic 373.6 1.6630 # SOURCE1 501 0.0086 + bond_coeff @bond:n3-py harmonic 338.1 1.7003 # SOURCE4 6 0.0044 + bond_coeff @bond:n3-s harmonic 232.3 1.7920 # SOURCE3 3 0.0178 + bond_coeff @bond:n3-s4 harmonic 251.3 1.7610 # SOURCE3 6 0.0766 + bond_coeff @bond:n3-s6 harmonic 353.8 1.6320 # SOURCE1 99 0.0136 + bond_coeff @bond:n3-sh harmonic 265.9 1.7390 # SOURCE3 3 0.0154 + bond_coeff @bond:n3-ss harmonic 277.9 1.7220 # SOURCE3 5 0.0207 + bond_coeff @bond:n3-sy harmonic 297.3 1.6964 # SOURCE4 226 0.0081 + bond_coeff @bond:n4-n4 harmonic 349.9 1.4840 # SOURCE3 4 0.0089 + bond_coeff @bond:n4-na harmonic 407.0 1.4350 # SOURCE3 9 0.0390 + bond_coeff @bond:n4-nh harmonic 369.7 1.4660 # SOURCE3 5 0.0108 + bond_coeff @bond:n4-no harmonic 354.2 1.4800 # SOUECE3 1 + bond_coeff @bond:n4-o harmonic 463.6 1.3610 # SOURCE3 3 0.0041 + bond_coeff @bond:n4-oh harmonic 408.2 1.4000 # SOURCE3 3 0.0115 + bond_coeff @bond:n4-os harmonic 381.8 1.4210 # SOURCE3 5 0.0249 + bond_coeff @bond:n4-p2 harmonic 185.9 1.9420 # SOURCE3 10 0.0643 + bond_coeff @bond:n4-p3 harmonic 215.1 1.8800 # SOURCE3 5 0.0146 + bond_coeff @bond:n4-p4 harmonic 187.6 1.9380 # SOURCE3 1 0.0000 + bond_coeff @bond:n4-p5 harmonic 242.9 1.8300 # SOURCE3 5 0.0087 + bond_coeff @bond:n4-py harmonic 204.2 1.9020 # SOURCE3 4 0.0000 + bond_coeff @bond:n4-s harmonic 210.3 1.8320 # SOURCE3 3 0.0004 + bond_coeff @bond:n4-s4 harmonic 151.0 1.9720 # SOURCE3 3 0.0198 + bond_coeff @bond:n4-s6 harmonic 172.7 1.9140 # SOURCE3 5 0.0432 + bond_coeff @bond:n4-sh harmonic 221.5 1.8110 # SOURCE3 3 0.0027 + bond_coeff @bond:n4-ss harmonic 221.0 1.8120 # SOURCE3 5 0.0064 + bond_coeff @bond:na-na harmonic 453.3 1.4010 # SOURCE1 40 0.0000 + bond_coeff @bond:na-nb harmonic 546.5 1.3440 # SOURCE4 5 0.0070 + bond_coeff @bond:na-nc harmonic 535.7 1.3500 # SOURCE3 152 0.0180 + bond_coeff @bond:na-nd harmonic 535.7 1.3500 # SOURCE3 152 0.0180 + bond_coeff @bond:na-nh harmonic 453.3 1.4010 # SOURCE1 40 0.0000 + bond_coeff @bond:na-no harmonic 401.9 1.4390 # SOURCE3 9 0.0289 + bond_coeff @bond:na-o harmonic 644.3 1.2650 # SOURCE1 25 0.0347 + bond_coeff @bond:na-oh harmonic 412.2 1.3970 # SOURCE3 9 0.0217 + bond_coeff @bond:na-os harmonic 355.2 1.4440 # SOURCE3 45 0.0423 + bond_coeff @bond:na-p2 harmonic 297.8 1.7490 # SOURCE3 11 0.0192 + bond_coeff @bond:na-p3 harmonic 288.0 1.7620 # SOURCE3 8 0.0113 + bond_coeff @bond:na-p4 harmonic 492.4 1.5640 # SOURCE3 5 0.2161 + bond_coeff @bond:na-p5 harmonic 325.3 1.7150 # SOURCE3 11 0.0238 + bond_coeff @bond:na-pc harmonic 311.1 1.7320 # SOURCE3 81 0.0207 + bond_coeff @bond:na-pd harmonic 311.1 1.7320 # SOURCE3 81 same_as_na-pc + bond_coeff @bond:na-py harmonic 327.8 1.7120 # SOURCE3 2 0.0000 + bond_coeff @bond:na-s harmonic 248.7 1.7650 # SOURCE3 8 0.0095 + bond_coeff @bond:na-s4 harmonic 231.7 1.7930 # SOURCE3 10 0.0421 + bond_coeff @bond:na-s6 harmonic 274.3 1.7270 # SOURCE3 10 0.0201 + bond_coeff @bond:na-sh harmonic 278.6 1.7210 # SOURCE3 9 0.0113 + bond_coeff @bond:na-ss harmonic 270.1 1.7330 # SOURCE3 38 0.0412 + bond_coeff @bond:na-sy harmonic 274.3 1.7270 # SOURCE3 1 + bond_coeff @bond:nb-nb harmonic 550.2 1.3420 # SOURCE1 15 0.0314 + bond_coeff @bond:nb-pb harmonic 461.1 1.5870 # SOURCE1 162 0.0091 + bond_coeff @bond:nc-nc harmonic 486.8 1.3790 # SOURCE3 9 0.0164 + bond_coeff @bond:nc-nd harmonic 602.9 1.3150 # SOURCE3 9 0.0221 + bond_coeff @bond:nc-os harmonic 414.9 1.3950 # SOURCE1 46 0.0188 + bond_coeff @bond:nc-ss harmonic 433.5 1.5600 # SOURCE1 74 0.0000 + bond_coeff @bond:nc-sy harmonic 439.8 1.5550 # SOURCE3 2 + bond_coeff @bond:nd-nd harmonic 486.8 1.3790 # SOURCE3 9 0.0164 + bond_coeff @bond:nd-os harmonic 414.9 1.3950 # SOURCE1 46 0.0188 + bond_coeff @bond:nd-ss harmonic 433.5 1.5600 # SOURCE1 74 0.0000 + bond_coeff @bond:nd-sy harmonic 439.8 1.5550 # SOURCE3 2 + bond_coeff @bond:ne-ne harmonic 355.3 1.4790 # SOURCE3 19 0.1705 + bond_coeff @bond:ne-nf harmonic 721.6 1.2635 # SOURCE4 25 0.0034 + bond_coeff @bond:ne-o harmonic 736.4 1.2280 # SOURCE3 40 0.0255 + bond_coeff @bond:ne-p2 harmonic 493.9 1.5630 # SOURCE3 14 0.1325 + bond_coeff @bond:ne-pe harmonic 327.8 1.7120 # SOURCE3 28 0.1076 + bond_coeff @bond:ne-px harmonic 336.6 1.7020 # SOURCE3 11 0.0883 + bond_coeff @bond:ne-py harmonic 425.4 1.6157 # SOURCE4 10 0.0094 + bond_coeff @bond:ne-s harmonic 463.5 1.5370 # SOURCE3 22 0.1708 + bond_coeff @bond:ne-sx harmonic 207.3 1.8380 # SOURCE3 7 0.1060 + bond_coeff @bond:ne-sy harmonic 257.1 1.7520 # SOURCE3 7 0.0814 + bond_coeff @bond:nf-nf harmonic 355.3 1.4790 # SOURCE3 19 same_as_ne-ne + bond_coeff @bond:nf-o harmonic 736.4 1.2280 # SOURCE3 40 same_as_ne-o + bond_coeff @bond:nf-p2 harmonic 493.9 1.5630 # SOURCE3 14 same_as_ne-p2 + bond_coeff @bond:nf-pf harmonic 327.8 1.7120 # SOURCE3 28 same_as_ne-pe + bond_coeff @bond:nf-px harmonic 336.6 1.7020 # SOURCE3 11 same_as_ne-px + bond_coeff @bond:nf-py harmonic 425.4 1.6157 # SOURCE4 10 same_as_ne-py + bond_coeff @bond:nf-s harmonic 463.5 1.5370 # SOURCE3 22 same_as_ne-s + bond_coeff @bond:nf-sx harmonic 207.3 1.8380 # SOURCE3 7 same_as_ne-sx + bond_coeff @bond:nf-sy harmonic 257.1 1.7520 # SOURCE3 7 same_as_ne-sy + bond_coeff @bond:nh-nh harmonic 453.3 1.4010 # SOURCE1 40 0.0000 + bond_coeff @bond:nh-no harmonic 477.4 1.3850 # SOURCE4 7 0.0036 + bond_coeff @bond:nh-o harmonic 596.2 1.2870 # SOURCE3 3 0.0450 + bond_coeff @bond:nh-oh harmonic 389.9 1.4144 # SOURCE4 19 0.0064 + bond_coeff @bond:nh-os harmonic 387.8 1.4161 # SOURCE4 6 0.0039 + bond_coeff @bond:nh-p2 harmonic 357.8 1.6790 # SOURCE3 17 0.0872 + bond_coeff @bond:nh-p3 harmonic 312.8 1.7300 # SOURCE3 3 0.0016 + bond_coeff @bond:nh-p4 harmonic 333.1 1.7060 # SOURCE3 3 0.0008 + bond_coeff @bond:nh-p5 harmonic 365.6 1.6710 # SOURCE3 3 0.0007 + bond_coeff @bond:nh-s harmonic 237.0 1.7840 # SOURCE3 3 0.0076 + bond_coeff @bond:nh-s4 harmonic 259.1 1.7490 # SOURCE3 3 0.0203 + bond_coeff @bond:nh-s6 harmonic 297.2 1.6965 # SOURCE4 33 0.0062 + bond_coeff @bond:nh-sh harmonic 288.3 1.7080 # SOURCE3 1 0.0000 + bond_coeff @bond:nh-ss harmonic 288.3 1.7080 # SOURCE1 52 0.0015 + bond_coeff @bond:nh-sy harmonic 283.5 1.7144 # SOURCE4 80 0.0066 + bond_coeff @bond:n-n1 harmonic 553.9 1.3400 # SOUECE3 1 + bond_coeff @bond:n-n2 harmonic 499.7 1.3710 # SOURCE3 9 0.0200 + bond_coeff @bond:n-n3 harmonic 443.3 1.4080 # SOURCE3 5 0.0087 + bond_coeff @bond:n-n4 harmonic 410.8 1.4320 # SOURCE3 5 0.0098 + bond_coeff @bond:n-n harmonic 469.7 1.3900 # SOURCE3 5 0.0038 + bond_coeff @bond:n-na harmonic 486.8 1.3790 # SOURCE3 11 0.0071 + bond_coeff @bond:n-nc harmonic 524.9 1.3561 # SOURCE4 63 0.0104 + bond_coeff @bond:n-nd harmonic 517.7 1.3603 # SOURCE4 13 0.0122 + bond_coeff @bond:n-nh harmonic 451.2 1.4025 # SOURCE4 20 0.0074 + bond_coeff @bond:n-no harmonic 381.2 1.4560 # SOURCE3 4 0.0327 + bond_coeff @bond:n-o harmonic 646.6 1.2640 # SOURCE3 9 0.0381 + bond_coeff @bond:n-oh harmonic 395.4 1.4100 # SOURCE3 6 0.0106 + bond_coeff @bond:no-no harmonic 138.3 1.8240 # SOURCE3 1 0.0000 + bond_coeff @bond:no-o harmonic 761.2 1.2190 # SOURCE1 1838 0.0049 + bond_coeff @bond:no-oh harmonic 400.5 1.4060 # SOURCE2 1 0.0000 + bond_coeff @bond:no-os harmonic 379.5 1.4229 # SOURCE4 53 0.0076 + bond_coeff @bond:no-os harmonic 379.5 1.4229 # SOURCE4 53 0.0076 + bond_coeff @bond:no-p2 harmonic 306.3 1.7380 # SOURCE3 10 0.2231 + bond_coeff @bond:no-p3 harmonic 234.7 1.8440 # SOURCE3 3 0.0005 + bond_coeff @bond:no-p4 harmonic 220.4 1.8700 # SOURCE3 3 0.0006 + bond_coeff @bond:no-p5 harmonic 240.5 1.8340 # SOURCE3 4 0.0020 + bond_coeff @bond:no-s harmonic 263.8 1.7420 # SOURCE3 2 0.0000 + bond_coeff @bond:n-os harmonic 395.0 1.4103 # SOURCE4 30 0.0112 + bond_coeff @bond:no-s4 harmonic 143.0 1.9960 # SOURCE3 3 0.0313 + bond_coeff @bond:no-s6 harmonic 149.6 1.9760 # SOURCE3 3 0.0520 + bond_coeff @bond:no-sh harmonic 225.4 1.8040 # SOURCE3 1 0.0000 + bond_coeff @bond:no-ss harmonic 212.4 1.8280 # SOURCE3 3 0.0244 + bond_coeff @bond:n-p2 harmonic 310.3 1.7330 # SOURCE3 8 0.0217 + bond_coeff @bond:n-p3 harmonic 282.2 1.7700 # SOURCE3 9 0.0118 + bond_coeff @bond:n-p4 harmonic 309.5 1.7340 # SOURCE3 1 0.0000 + bond_coeff @bond:n-p5 harmonic 331.3 1.7080 # SOURCE4 6 0.0022 + bond_coeff @bond:n-pc harmonic 304.8 1.7400 # SOURCE3 3 0.0010 + bond_coeff @bond:n-pd harmonic 304.8 1.7400 # SOURCE3 3 same_as_n-pc + bond_coeff @bond:n-s harmonic 247.5 1.7670 # SOURCE3 3 0.0011 + bond_coeff @bond:n-s4 harmonic 238.2 1.7820 # SOURCE3 4 0.0214 + bond_coeff @bond:n-s6 harmonic 283.0 1.7151 # SOURCE4 13 0.0138 + bond_coeff @bond:n-sh harmonic 273.6 1.7280 # SOURCE3 4 0.0128 + bond_coeff @bond:n-ss harmonic 281.6 1.7170 # SOURCE3 7 0.0133 + bond_coeff @bond:n-sy harmonic 282.9 1.7152 # SOURCE4 51 0.0079 + bond_coeff @bond:oh-oh harmonic 340.5 1.4690 # SOURCE3 1 0.0000 + bond_coeff @bond:oh-os harmonic 355.8 1.4547 # SOURCE4 19 0.0050 + bond_coeff @bond:oh-p2 harmonic 316.8 1.6300 # SOURCE3 8 0.0916 + bond_coeff @bond:oh-p3 harmonic 278.8 1.6770 # SOURCE3 3 0.0148 + bond_coeff @bond:oh-p4 harmonic 307.4 1.6410 # SOURCE3 4 0.0092 + bond_coeff @bond:oh-p5 harmonic 321.2 1.6250 # SOURCE3 92 0.0451 + bond_coeff @bond:oh-py harmonic 332.1 1.6130 # SOURCE3 79 0.0138 + bond_coeff @bond:oh-s harmonic 190.0 1.8120 # SOURCE3 2 0.0000 + bond_coeff @bond:oh-s4 harmonic 256.3 1.6954 # SOURCE4 10 0.0091 + bond_coeff @bond:oh-s6 harmonic 344.1 1.5880 # SOURCE3 13 0.0091 + bond_coeff @bond:oh-sh harmonic 258.6 1.6920 # SOURCE3 2 0.0003 + bond_coeff @bond:oh-ss harmonic 265.6 1.6820 # SOURCE3 4 0.0131 + bond_coeff @bond:oh-sy harmonic 290.4 1.6490 # SOURCE4 33 0.0044 + bond_coeff @bond:o-o harmonic 384.3 1.4300 # SOURCE3 2 0.0500 + bond_coeff @bond:o-oh harmonic 294.6 1.5170 # SOURCE3 2 0.0000 + bond_coeff @bond:o-os harmonic 306.3 1.5040 # SOURCE3 3 0.0117 + bond_coeff @bond:o-p2 harmonic 449.7 1.5080 # SOURCE3 17 0.0306 + bond_coeff @bond:o-p3 harmonic 440.4 1.5150 # SOURCE3 35 0.0297 + bond_coeff @bond:o-p4 harmonic 456.4 1.5030 # SOURCE3 42 0.0749 + bond_coeff @bond:o-p5 harmonic 487.7 1.4810 # SOURCE1 263 0.0205 + bond_coeff @bond:o-pe harmonic 432.6 1.5210 # SOURCE3 20 0.0171 + bond_coeff @bond:o-pf harmonic 432.6 1.5210 # SOURCE3 20 same_as_o-pe + bond_coeff @bond:o-px harmonic 459.2 1.5010 # SOURCE3 37 0.0160 + bond_coeff @bond:o-py harmonic 477.5 1.4880 # SOURCE3 63 0.0091 + bond_coeff @bond:o-s harmonic 194.8 1.8020 # SOURCE3 2 0.0000 + bond_coeff @bond:o-s2 harmonic 333.6 1.5990 # SOURCE3 3 0.0707 + bond_coeff @bond:o-s4 harmonic 448.7 1.4970 # SOURCE1 90 0.0000 + bond_coeff @bond:o-s6 harmonic 541.1 1.4360 # SOURCE1 1038 0.0128 + bond_coeff @bond:o-sh harmonic 328.0 1.6050 # SOURCE3 2 0.0000 + bond_coeff @bond:os-os harmonic 343.6 1.4660 # SOURCE1 20 0.0067 + bond_coeff @bond:os-p2 harmonic 371.9 1.5730 # SOURCE1 16 0.0000 + bond_coeff @bond:os-p3 harmonic 272.2 1.6860 # SOURCE3 6 0.0201 + bond_coeff @bond:os-p4 harmonic 311.6 1.6360 # SOURCE3 4 0.0057 + bond_coeff @bond:os-p5 harmonic 342.5 1.6020 # SOURCE1 248 0.0400 + bond_coeff @bond:os-py harmonic 328.5 1.6170 # SOURCE3 17 0.0139 + bond_coeff @bond:os-s harmonic 195.8 1.8000 # SOURCE3 3 0.0052 + bond_coeff @bond:o-ss harmonic 398.5 1.5370 # SOURCE3 3 0.0501 + bond_coeff @bond:os-s4 harmonic 253.9 1.6990 # SOURCE3 8 0.0223 + bond_coeff @bond:os-s6 harmonic 355.0 1.5770 # SOURCE1 75 0.0030 + bond_coeff @bond:os-sh harmonic 273.6 1.6710 # SOURCE3 3 0.0106 + bond_coeff @bond:os-ss harmonic 250.5 1.7040 # SOURCE3 9 0.0277 + bond_coeff @bond:os-sy harmonic 253.9 1.6990 # SOURCE3 1 0.0000 + bond_coeff @bond:o-sx harmonic 434.2 1.5080 # SOURCE3 40 0.0130 + bond_coeff @bond:o-sy harmonic 493.0 1.4660 # SOURCE3 92 0.0114 + bond_coeff @bond:p2-p2 harmonic 490.3 1.7860 # SOURCE3 25 0.3488 + bond_coeff @bond:p2-p3 harmonic 211.9 2.1520 # SOURCE3 9 0.1777 + bond_coeff @bond:p2-p4 harmonic 200.4 2.1790 # SOUECE3 1 + bond_coeff @bond:p2-p5 harmonic 199.9 2.1800 # SOUECE3 1 + bond_coeff @bond:p2-pe harmonic 401.6 1.8670 # SOURCE3 16 0.3571 + bond_coeff @bond:p2-pf harmonic 401.6 1.8670 # SOURCE3 16 same_as_p2-pe + bond_coeff @bond:p2-s harmonic 361.6 1.7720 # SOURCE3 26 0.3014 + bond_coeff @bond:p2-s4 harmonic 139.4 2.1900 # SOUECE3 1 + bond_coeff @bond:p2-s6 harmonic 142.3 2.1800 # SOUECE3 1 + bond_coeff @bond:p2-sh harmonic 224.0 1.9710 # SOURCE3 10 0.2829 + bond_coeff @bond:p2-ss harmonic 226.6 1.9660 # SOURCE3 10 0.2739 + bond_coeff @bond:p3-p3 harmonic 186.5 2.2140 # SOURCE1 41 0.0000 + bond_coeff @bond:p3-p4 harmonic 185.7 2.2160 # SOURCE3 3 0.0011 + bond_coeff @bond:p3-p5 harmonic 186.9 2.2130 # SOURCE3 9 0.0265 + bond_coeff @bond:p3-s harmonic 179.7 2.0700 # SOUECE3 1 + bond_coeff @bond:p3-s4 harmonic 173.2 2.0870 # SOURCE3 8 0.2235 + bond_coeff @bond:p3-s6 harmonic 176.9 2.0770 # SOURCE3 11 0.1420 + bond_coeff @bond:p3-sh harmonic 157.3 2.1320 # SOURCE3 3 0.0078 + bond_coeff @bond:p3-ss harmonic 161.0 2.1210 # SOURCE3 3 0.0059 + bond_coeff @bond:p4-p4 harmonic 273.1 2.0340 # SOURCE1 1 0.0000 + bond_coeff @bond:p4-p5 harmonic 178.0 2.2370 # SOUECE3 1 + bond_coeff @bond:p4-s harmonic 152.7 2.1460 # SOURCE3 5 0.0601 + bond_coeff @bond:p4-s4 harmonic 123.2 2.2510 # SOUECE3 1 + bond_coeff @bond:p4-s6 harmonic 118.9 2.2690 # SOUECE3 1 + bond_coeff @bond:p4-sh harmonic 163.1 2.1150 # SOURCE3 4 0.0008 + bond_coeff @bond:p4-ss harmonic 167.0 2.1040 # SOURCE3 4 0.0044 + bond_coeff @bond:p5-p5 harmonic 261.4 2.0540 # SOURCE1 1 0.0000 + bond_coeff @bond:p5-s harmonic 250.8 1.9220 # SOURCE1 89 0.0140 + bond_coeff @bond:p5-s4 harmonic 191.9 2.0400 # SOUECE3 1 + bond_coeff @bond:p5-s6 harmonic 191.9 2.0400 # SOUECE3 1 + bond_coeff @bond:p5-sh harmonic 175.0 2.0820 # SOURCE3 3 0.0035 + bond_coeff @bond:p5-ss harmonic 163.1 2.1149 # SOURCE4 24 0.0106 + bond_coeff @bond:pe-pe harmonic 240.7 2.0920 # SOURCE3 7 0.1369 + bond_coeff @bond:pe-pf harmonic 260.8 2.0550 # SOURCE3 1 0.0000 + bond_coeff @bond:pe-px harmonic 291.4 2.0050 # SOURCE3 12 0.2609 + bond_coeff @bond:pe-py harmonic 278.6 2.0250 # SOURCE3 12 0.2617 + bond_coeff @bond:pe-s harmonic 374.7 1.7580 # SOURCE3 31 0.3197 + bond_coeff @bond:pe-sx harmonic 145.9 2.1680 # SOURCE3 9 0.1743 + bond_coeff @bond:pe-sy harmonic 133.0 2.2130 # SOURCE3 6 0.0127 + bond_coeff @bond:pf-pf harmonic 240.7 2.0920 # SOURCE3 7 same_as_pe-pe + bond_coeff @bond:pf-px harmonic 291.4 2.0050 # SOURCE3 12 same_as_pe-px + bond_coeff @bond:pf-py harmonic 278.6 2.0250 # SOURCE3 12 same_as_pe-py + bond_coeff @bond:pf-s harmonic 374.7 1.7580 # SOURCE3 31 same_as_pe-s + bond_coeff @bond:pf-sx harmonic 145.9 2.1680 # SOURCE3 9 same_as_pe-sx + bond_coeff @bond:pf-sy harmonic 133.0 2.2130 # SOURCE3 6 same_as_pe-sy + bond_coeff @bond:px-py harmonic 192.3 2.1990 # SOURCE3 5 0.0238 + bond_coeff @bond:px-sx harmonic 125.4 2.2420 # SOURCE3 3 0.0119 + bond_coeff @bond:px-sy harmonic 123.7 2.2490 # SOURCE3 3 0.0272 + bond_coeff @bond:py-py harmonic 197.5 2.1860 # SOURCE3 8 0.0132 + bond_coeff @bond:py-sx harmonic 121.2 2.2590 # SOURCE3 7 0.0603 + bond_coeff @bond:py-sy harmonic 141.7 2.1820 # SOURCE3 5 0.0047 + bond_coeff @bond:s4-s4 harmonic 151.5 2.0800 # SOUECE3 1 + bond_coeff @bond:s4-s6 harmonic 151.5 2.0800 # SOUECE3 1 + bond_coeff @bond:s4-sh harmonic 125.7 2.1680 # SOURCE3 3 0.0227 + bond_coeff @bond:s4-ss harmonic 126.2 2.1660 # SOURCE3 5 0.0247 + bond_coeff @bond:s6-s6 harmonic 151.5 2.0800 # SOUECE3 1 + bond_coeff @bond:s6-sh harmonic 142.6 2.1080 # SOURCE3 3 0.0144 + bond_coeff @bond:s6-ss harmonic 139.6 2.1180 # SOURCE3 5 0.0209 + bond_coeff @bond:sh-sh harmonic 158.9 2.0580 # SOURCE2 1 0.0000 + bond_coeff @bond:sh-ss harmonic 155.8 2.0670 # SOURCE3 3 0.0029 + bond_coeff @bond:s-s harmonic 169.0 2.0300 # SOURCE3 1 0.0000 + bond_coeff @bond:s-s2 harmonic 229.2 1.8970 # SOURCE1 5 0.0000 + bond_coeff @bond:s-s4 harmonic 152.8 2.0760 # SOURCE3 4 0.0345 + bond_coeff @bond:s-s6 harmonic 166.0 2.0380 # SOURCE3 3 0.0311 + bond_coeff @bond:s-sh harmonic 142.0 2.1100 # SOURCE3 2 0.0000 + bond_coeff @bond:s-ss harmonic 148.5 2.0890 # SOURCE3 1 0.0000 + bond_coeff @bond:ss-ss harmonic 161.7 2.0500 # SOURCE1 225 0.0015 + bond_coeff @bond:sx-sx harmonic 80.9 2.3910 # SOURCE3 3 0.0185 + bond_coeff @bond:sx-sy harmonic 105.3 2.2550 # SOURCE3 5 0.0737 + bond_coeff @bond:sy-sy harmonic 106.4 2.2500 # SOURCE3 3 0.0289 + } # (end of bond_coeffs) + + write_once("Data Bonds By Type") { + @bond:ow-hw @atom:ow @atom:hw + @bond:br-br @atom:br @atom:br + @bond:br-c1 @atom:br @atom:c1 + @bond:br-c2 @atom:br @atom:c2 + @bond:br-c @atom:br @atom:c + @bond:br-c3 @atom:br @atom:c3 + @bond:br-ca @atom:br @atom:ca + @bond:br-cc @atom:br @atom:cc + @bond:br-cx @atom:br @atom:cx + @bond:br-i @atom:br @atom:i + @bond:br-n1 @atom:br @atom:n1 + @bond:br-n2 @atom:br @atom:n2 + @bond:br-n @atom:br @atom:n + @bond:br-n3 @atom:br @atom:n3 + @bond:br-n4 @atom:br @atom:n4 + @bond:br-na @atom:br @atom:na + @bond:br-nh @atom:br @atom:nh + @bond:br-no @atom:br @atom:no + @bond:br-o @atom:br @atom:o + @bond:br-oh @atom:br @atom:oh + @bond:br-os @atom:br @atom:os + @bond:br-p2 @atom:br @atom:p2 + @bond:br-p3 @atom:br @atom:p3 + @bond:br-p4 @atom:br @atom:p4 + @bond:br-p5 @atom:br @atom:p5 + @bond:br-s @atom:br @atom:s + @bond:br-s4 @atom:br @atom:s4 + @bond:br-s6 @atom:br @atom:s6 + @bond:br-sh @atom:br @atom:sh + @bond:br-ss @atom:br @atom:ss + @bond:c1-c1 @atom:c1 @atom:c1 + @bond:c1-c2 @atom:c1 @atom:c2 + @bond:c1-c3 @atom:c1 @atom:c3 + @bond:c1-ca @atom:c1 @atom:ca + @bond:c1-ce @atom:c1 @atom:ce + @bond:c1-cg @atom:c1 @atom:cg + @bond:c1-ch @atom:c1 @atom:ch + @bond:c1-cl @atom:c1 @atom:cl + @bond:c1-cx @atom:c1 @atom:cx + @bond:c1-f @atom:c1 @atom:f + @bond:c1-ha @atom:c1 @atom:ha + @bond:c1-hc @atom:c1 @atom:hc + @bond:c1-i @atom:c1 @atom:i + @bond:c1-n1 @atom:c1 @atom:n1 + @bond:c1-n2 @atom:c1 @atom:n2 + @bond:c1-n3 @atom:c1 @atom:n3 + @bond:c1-n4 @atom:c1 @atom:n4 + @bond:c1-n @atom:c1 @atom:n + @bond:c1-na @atom:c1 @atom:na + @bond:c1-ne @atom:c1 @atom:ne + @bond:c1-nf @atom:c1 @atom:nf + @bond:c1-nh @atom:c1 @atom:nh + @bond:c1-no @atom:c1 @atom:no + @bond:c1-o @atom:c1 @atom:o + @bond:c1-oh @atom:c1 @atom:oh + @bond:c1-os @atom:c1 @atom:os + @bond:c1-p2 @atom:c1 @atom:p2 + @bond:c1-p3 @atom:c1 @atom:p3 + @bond:c1-p4 @atom:c1 @atom:p4 + @bond:c1-p5 @atom:c1 @atom:p5 + @bond:c1-s2 @atom:c1 @atom:s2 + @bond:c1-s @atom:c1 @atom:s + @bond:c1-s4 @atom:c1 @atom:s4 + @bond:c1-s6 @atom:c1 @atom:s6 + @bond:c1-sh @atom:c1 @atom:sh + @bond:c1-ss @atom:c1 @atom:ss + @bond:c2-c2 @atom:c2 @atom:c2 + @bond:c2-c3 @atom:c2 @atom:c3 + @bond:c2-ca @atom:c2 @atom:ca + @bond:c2-cc @atom:c2 @atom:cc + @bond:c2-cd @atom:c2 @atom:cd + @bond:c2-ce @atom:c2 @atom:ce + @bond:c2-cf @atom:c2 @atom:cf + @bond:c2-cl @atom:c2 @atom:cl + @bond:c2-cu @atom:c2 @atom:cu + @bond:c2-cx @atom:c2 @atom:cx + @bond:c2-cy @atom:c2 @atom:cy + @bond:c2-f @atom:c2 @atom:f + @bond:c2-h4 @atom:c2 @atom:h4 + @bond:c2-h5 @atom:c2 @atom:h5 + @bond:c2-ha @atom:c2 @atom:ha + @bond:c2-hc @atom:c2 @atom:hc + @bond:c2-hx @atom:c2 @atom:hx + @bond:c2-i @atom:c2 @atom:i + @bond:c2-n1 @atom:c2 @atom:n1 + @bond:c2-n2 @atom:c2 @atom:n2 + @bond:c2-n3 @atom:c2 @atom:n3 + @bond:c2-n @atom:c2 @atom:n + @bond:c2-n4 @atom:c2 @atom:n4 + @bond:c2-na @atom:c2 @atom:na + @bond:c2-nc @atom:c2 @atom:nc + @bond:c2-nd @atom:c2 @atom:nd + @bond:c2-ne @atom:c2 @atom:ne + @bond:c2-nf @atom:c2 @atom:nf + @bond:c2-nh @atom:c2 @atom:nh + @bond:c2-no @atom:c2 @atom:no + @bond:c2-o @atom:c2 @atom:o + @bond:c2-oh @atom:c2 @atom:oh + @bond:c2-os @atom:c2 @atom:os + @bond:c2-p2 @atom:c2 @atom:p2 + @bond:c2-p3 @atom:c2 @atom:p3 + @bond:c2-p4 @atom:c2 @atom:p4 + @bond:c2-p5 @atom:c2 @atom:p5 + @bond:c2-pe @atom:c2 @atom:pe + @bond:c2-pf @atom:c2 @atom:pf + @bond:c2-s2 @atom:c2 @atom:s2 + @bond:c2-s @atom:c2 @atom:s + @bond:c2-s4 @atom:c2 @atom:s4 + @bond:c2-s6 @atom:c2 @atom:s6 + @bond:c2-sh @atom:c2 @atom:sh + @bond:c2-ss @atom:c2 @atom:ss + @bond:c3-c3 @atom:c3 @atom:c3 + @bond:c3-ca @atom:c3 @atom:ca + @bond:c3-cc @atom:c3 @atom:cc + @bond:c3-cd @atom:c3 @atom:cd + @bond:c3-ce @atom:c3 @atom:ce + @bond:c3-cf @atom:c3 @atom:cf + @bond:c3-cl @atom:c3 @atom:cl + @bond:c3-cu @atom:c3 @atom:cu + @bond:c3-cv @atom:c3 @atom:cv + @bond:c3-cx @atom:c3 @atom:cx + @bond:c3-cy @atom:c3 @atom:cy + @bond:c3-f @atom:c3 @atom:f + @bond:c3-h1 @atom:c3 @atom:h1 + @bond:c3-h2 @atom:c3 @atom:h2 + @bond:c3-h3 @atom:c3 @atom:h3 + @bond:c3-hc @atom:c3 @atom:hc + @bond:c3-hx @atom:c3 @atom:hx + @bond:c3-i @atom:c3 @atom:i + @bond:c3-n1 @atom:c3 @atom:n1 + @bond:c3-n2 @atom:c3 @atom:n2 + @bond:c3-n @atom:c3 @atom:n + @bond:c3-n3 @atom:c3 @atom:n3 + @bond:c3-n4 @atom:c3 @atom:n4 + @bond:c3-na @atom:c3 @atom:na + @bond:c3-nc @atom:c3 @atom:nc + @bond:c3-nd @atom:c3 @atom:nd + @bond:c3-nh @atom:c3 @atom:nh + @bond:c3-no @atom:c3 @atom:no + @bond:c3-o @atom:c3 @atom:o + @bond:c3-oh @atom:c3 @atom:oh + @bond:c3-os @atom:c3 @atom:os + @bond:c3-p2 @atom:c3 @atom:p2 + @bond:c3-p3 @atom:c3 @atom:p3 + @bond:c3-p4 @atom:c3 @atom:p4 + @bond:c3-p5 @atom:c3 @atom:p5 + @bond:c3-px @atom:c3 @atom:px + @bond:c3-py @atom:c3 @atom:py + @bond:c3-s @atom:c3 @atom:s + @bond:c3-s4 @atom:c3 @atom:s4 + @bond:c3-s6 @atom:c3 @atom:s6 + @bond:c3-sh @atom:c3 @atom:sh + @bond:c3-ss @atom:c3 @atom:ss + @bond:c3-sx @atom:c3 @atom:sx + @bond:c3-sy @atom:c3 @atom:sy + @bond:ca-ca @atom:ca @atom:ca + @bond:ca-cc @atom:ca @atom:cc + @bond:ca-cd @atom:ca @atom:cd + @bond:ca-ce @atom:ca @atom:ce + @bond:ca-cf @atom:ca @atom:cf + @bond:ca-cg @atom:ca @atom:cg + @bond:ca-ch @atom:ca @atom:ch + @bond:ca-cl @atom:ca @atom:cl + @bond:ca-cp @atom:ca @atom:cp + @bond:ca-cq @atom:ca @atom:cq + @bond:ca-cx @atom:ca @atom:cx + @bond:ca-cy @atom:ca @atom:cy + @bond:ca-f @atom:ca @atom:f + @bond:ca-h4 @atom:ca @atom:h4 + @bond:ca-h5 @atom:ca @atom:h5 + @bond:ca-ha @atom:ca @atom:ha + @bond:ca-i @atom:ca @atom:i + @bond:ca-n1 @atom:ca @atom:n1 + @bond:ca-n2 @atom:ca @atom:n2 + @bond:ca-n @atom:ca @atom:n + @bond:ca-n4 @atom:ca @atom:n4 + @bond:ca-na @atom:ca @atom:na + @bond:ca-nb @atom:ca @atom:nb + @bond:ca-nc @atom:ca @atom:nc + @bond:ca-nd @atom:ca @atom:nd + @bond:ca-ne @atom:ca @atom:ne + @bond:ca-nf @atom:ca @atom:nf + @bond:ca-nh @atom:ca @atom:nh + @bond:ca-no @atom:ca @atom:no + @bond:ca-o @atom:ca @atom:o + @bond:ca-oh @atom:ca @atom:oh + @bond:ca-os @atom:ca @atom:os + @bond:ca-p2 @atom:ca @atom:p2 + @bond:ca-p3 @atom:ca @atom:p3 + @bond:ca-p4 @atom:ca @atom:p4 + @bond:ca-p5 @atom:ca @atom:p5 + @bond:ca-pe @atom:ca @atom:pe + @bond:ca-pf @atom:ca @atom:pf + @bond:ca-px @atom:ca @atom:px + @bond:ca-py @atom:ca @atom:py + @bond:ca-s @atom:ca @atom:s + @bond:ca-s4 @atom:ca @atom:s4 + @bond:ca-s6 @atom:ca @atom:s6 + @bond:ca-sh @atom:ca @atom:sh + @bond:ca-ss @atom:ca @atom:ss + @bond:ca-sx @atom:ca @atom:sx + @bond:ca-sy @atom:ca @atom:sy + @bond:c-c1 @atom:c @atom:c1 + @bond:c-c2 @atom:c @atom:c2 + @bond:c-c @atom:c @atom:c + @bond:c-c3 @atom:c @atom:c3 + @bond:c-ca @atom:c @atom:ca + @bond:c-cc @atom:c @atom:cc + @bond:cc-cc @atom:cc @atom:cc + @bond:cc-cd @atom:cc @atom:cd + @bond:cc-ce @atom:cc @atom:ce + @bond:cc-cf @atom:cc @atom:cf + @bond:cc-cg @atom:cc @atom:cg + @bond:cc-ch @atom:cc @atom:ch + @bond:cc-cl @atom:cc @atom:cl + @bond:cc-cx @atom:cc @atom:cx + @bond:c-cd @atom:c @atom:cd + @bond:c-ce @atom:c @atom:ce + @bond:c-cf @atom:c @atom:cf + @bond:cc-f @atom:cc @atom:f + @bond:c-cg @atom:c @atom:cg + @bond:c-ch @atom:c @atom:ch + @bond:cc-h4 @atom:cc @atom:h4 + @bond:cc-h5 @atom:cc @atom:h5 + @bond:cc-ha @atom:cc @atom:ha + @bond:c-cl @atom:c @atom:cl + @bond:cc-n2 @atom:cc @atom:n2 + @bond:cc-n @atom:cc @atom:n + @bond:cc-n4 @atom:cc @atom:n4 + @bond:cc-na @atom:cc @atom:na + @bond:cc-nc @atom:cc @atom:nc + @bond:cc-nd @atom:cc @atom:nd + @bond:cc-ne @atom:cc @atom:ne + @bond:cc-nf @atom:cc @atom:nf + @bond:cc-nh @atom:cc @atom:nh + @bond:cc-no @atom:cc @atom:no + @bond:cc-oh @atom:cc @atom:oh + @bond:cc-os @atom:cc @atom:os + @bond:cc-pd @atom:cc @atom:pd + @bond:cc-sh @atom:cc @atom:sh + @bond:cc-ss @atom:cc @atom:ss + @bond:cc-sx @atom:cc @atom:sx + @bond:cc-sy @atom:cc @atom:sy + @bond:c-cu @atom:c @atom:cu + @bond:c-cx @atom:c @atom:cx + @bond:c-cy @atom:c @atom:cy + @bond:cd-cd @atom:cd @atom:cd + @bond:cd-ce @atom:cd @atom:ce + @bond:cd-cf @atom:cd @atom:cf + @bond:cd-cg @atom:cd @atom:cg + @bond:cd-ch @atom:cd @atom:ch + @bond:cd-cl @atom:cd @atom:cl + @bond:cd-cx @atom:cd @atom:cx + @bond:cd-cy @atom:cd @atom:cy + @bond:cd-h4 @atom:cd @atom:h4 + @bond:cd-h5 @atom:cd @atom:h5 + @bond:cd-ha @atom:cd @atom:ha + @bond:cd-n2 @atom:cd @atom:n2 + @bond:cd-n @atom:cd @atom:n + @bond:cd-na @atom:cd @atom:na + @bond:cd-nc @atom:cd @atom:nc + @bond:cd-nd @atom:cd @atom:nd + @bond:cd-ne @atom:cd @atom:ne + @bond:cd-nh @atom:cd @atom:nh + @bond:cd-oh @atom:cd @atom:oh + @bond:cd-os @atom:cd @atom:os + @bond:cd-pc @atom:cd @atom:pc + @bond:cd-ss @atom:cd @atom:ss + @bond:cd-sy @atom:cd @atom:sy + @bond:ce-ce @atom:ce @atom:ce + @bond:ce-cf @atom:ce @atom:cf + @bond:ce-cg @atom:ce @atom:cg + @bond:ce-ch @atom:ce @atom:ch + @bond:ce-cl @atom:ce @atom:cl + @bond:ce-cx @atom:ce @atom:cx + @bond:ce-cy @atom:ce @atom:cy + @bond:ce-h4 @atom:ce @atom:h4 + @bond:ce-ha @atom:ce @atom:ha + @bond:ce-n1 @atom:ce @atom:n1 + @bond:ce-n2 @atom:ce @atom:n2 + @bond:ce-n @atom:ce @atom:n + @bond:ce-na @atom:ce @atom:na + @bond:ce-ne @atom:ce @atom:ne + @bond:ce-nf @atom:ce @atom:nf + @bond:ce-nh @atom:ce @atom:nh + @bond:ce-oh @atom:ce @atom:oh + @bond:ce-os @atom:ce @atom:os + @bond:ce-p2 @atom:ce @atom:p2 + @bond:ce-pe @atom:ce @atom:pe + @bond:ce-px @atom:ce @atom:px + @bond:ce-py @atom:ce @atom:py + @bond:ce-s @atom:ce @atom:s + @bond:ce-ss @atom:ce @atom:ss + @bond:ce-sx @atom:ce @atom:sx + @bond:ce-sy @atom:ce @atom:sy + @bond:c-f @atom:c @atom:f + @bond:cf-cf @atom:cf @atom:cf + @bond:cf-cg @atom:cf @atom:cg + @bond:cf-ch @atom:cf @atom:ch + @bond:cf-h4 @atom:cf @atom:h4 + @bond:cf-ha @atom:cf @atom:ha + @bond:cf-n1 @atom:cf @atom:n1 + @bond:cf-n2 @atom:cf @atom:n2 + @bond:cf-n @atom:cf @atom:n + @bond:cf-ne @atom:cf @atom:ne + @bond:cf-nf @atom:cf @atom:nf + @bond:cf-nh @atom:cf @atom:nh + @bond:cf-oh @atom:cf @atom:oh + @bond:cf-os @atom:cf @atom:os + @bond:cf-p2 @atom:cf @atom:p2 + @bond:cf-pf @atom:cf @atom:pf + @bond:cf-px @atom:cf @atom:px + @bond:cf-py @atom:cf @atom:py + @bond:cf-s @atom:cf @atom:s + @bond:cf-sx @atom:cf @atom:sx + @bond:cf-sy @atom:cf @atom:sy + @bond:cg-cg @atom:cg @atom:cg + @bond:cg-ch @atom:cg @atom:ch + @bond:cg-n1 @atom:cg @atom:n1 + @bond:cg-ne @atom:cg @atom:ne + @bond:cg-pe @atom:cg @atom:pe + @bond:c-h4 @atom:c @atom:h4 + @bond:c-h5 @atom:c @atom:h5 + @bond:c-ha @atom:c @atom:ha + @bond:ch-ch @atom:ch @atom:ch + @bond:ch-n1 @atom:ch @atom:n1 + @bond:ch-nf @atom:ch @atom:nf + @bond:ch-pf @atom:ch @atom:pf + @bond:c-i @atom:c @atom:i + @bond:cl-cl @atom:cl @atom:cl + @bond:cl-cx @atom:cl @atom:cx + @bond:cl-cy @atom:cl @atom:cy + @bond:cl-f @atom:cl @atom:f + @bond:cl-i @atom:cl @atom:i + @bond:cl-n1 @atom:cl @atom:n1 + @bond:cl-n2 @atom:cl @atom:n2 + @bond:cl-n3 @atom:cl @atom:n3 + @bond:cl-n @atom:cl @atom:n + @bond:cl-n4 @atom:cl @atom:n4 + @bond:cl-na @atom:cl @atom:na + @bond:cl-nh @atom:cl @atom:nh + @bond:cl-no @atom:cl @atom:no + @bond:cl-o @atom:cl @atom:o + @bond:cl-oh @atom:cl @atom:oh + @bond:cl-os @atom:cl @atom:os + @bond:cl-p2 @atom:cl @atom:p2 + @bond:cl-p3 @atom:cl @atom:p3 + @bond:cl-p4 @atom:cl @atom:p4 + @bond:cl-p5 @atom:cl @atom:p5 + @bond:cl-pb @atom:cl @atom:pb + @bond:cl-s @atom:cl @atom:s + @bond:cl-s2 @atom:cl @atom:s2 + @bond:cl-s4 @atom:cl @atom:s4 + @bond:cl-s6 @atom:cl @atom:s6 + @bond:cl-sh @atom:cl @atom:sh + @bond:cl-ss @atom:cl @atom:ss + @bond:cl-sx @atom:cl @atom:sx + @bond:cl-sy @atom:cl @atom:sy + @bond:c-n2 @atom:c @atom:n2 + @bond:c-n4 @atom:c @atom:n4 + @bond:c-n @atom:c @atom:n + @bond:c-nc @atom:c @atom:nc + @bond:c-nd @atom:c @atom:nd + @bond:c-ne @atom:c @atom:ne + @bond:c-nf @atom:c @atom:nf + @bond:c-no @atom:c @atom:no + @bond:c-o @atom:c @atom:o + @bond:c-oh @atom:c @atom:oh + @bond:c-os @atom:c @atom:os + @bond:c-p2 @atom:c @atom:p2 + @bond:c-p3 @atom:c @atom:p3 + @bond:c-p4 @atom:c @atom:p4 + @bond:c-p5 @atom:c @atom:p5 + @bond:cp-cp @atom:cp @atom:cp + @bond:cp-cq @atom:cp @atom:cq + @bond:c-pe @atom:c @atom:pe + @bond:c-pf @atom:c @atom:pf + @bond:cp-na @atom:cp @atom:na + @bond:cp-nb @atom:cp @atom:nb + @bond:c-px @atom:c @atom:px + @bond:c-py @atom:c @atom:py + @bond:cq-cq @atom:cq @atom:cq + @bond:c-s @atom:c @atom:s + @bond:c-s4 @atom:c @atom:s4 + @bond:c-s6 @atom:c @atom:s6 + @bond:c-sh @atom:c @atom:sh + @bond:c-ss @atom:c @atom:ss + @bond:c-sx @atom:c @atom:sx + @bond:c-sy @atom:c @atom:sy + @bond:cu-cu @atom:cu @atom:cu + @bond:cu-cx @atom:cu @atom:cx + @bond:cu-ha @atom:cu @atom:ha + @bond:cv-cv @atom:cv @atom:cv + @bond:cv-cy @atom:cv @atom:cy + @bond:cv-ha @atom:cv @atom:ha + @bond:cx-cv @atom:cx @atom:cv + @bond:cx-cx @atom:cx @atom:cx + @bond:cx-cy @atom:cx @atom:cy + @bond:cx-f @atom:cx @atom:f + @bond:cx-h1 @atom:cx @atom:h1 + @bond:cx-h2 @atom:cx @atom:h2 + @bond:cx-hc @atom:cx @atom:hc + @bond:cx-hx @atom:cx @atom:hx + @bond:cx-n2 @atom:cx @atom:n2 + @bond:cx-n3 @atom:cx @atom:n3 + @bond:cx-n @atom:cx @atom:n + @bond:cx-na @atom:cx @atom:na + @bond:cx-nh @atom:cx @atom:nh + @bond:cx-oh @atom:cx @atom:oh + @bond:cx-os @atom:cx @atom:os + @bond:cx-p3 @atom:cx @atom:p3 + @bond:cx-s4 @atom:cx @atom:s4 + @bond:cx-s6 @atom:cx @atom:s6 + @bond:cx-ss @atom:cx @atom:ss + @bond:cy-cy @atom:cy @atom:cy + @bond:cy-f @atom:cy @atom:f + @bond:cy-h1 @atom:cy @atom:h1 + @bond:cy-h2 @atom:cy @atom:h2 + @bond:cy-hc @atom:cy @atom:hc + @bond:cy-n @atom:cy @atom:n + @bond:cy-n3 @atom:cy @atom:n3 + @bond:cy-oh @atom:cy @atom:oh + @bond:cy-os @atom:cy @atom:os + @bond:cy-s6 @atom:cy @atom:s6 + @bond:cy-ss @atom:cy @atom:ss + @bond:cz-nh @atom:cz @atom:nh + @bond:f-n1 @atom:f @atom:n1 + @bond:f-n2 @atom:f @atom:n2 + @bond:f-n3 @atom:f @atom:n3 + @bond:f-n @atom:f @atom:n + @bond:f-n4 @atom:f @atom:n4 + @bond:f-na @atom:f @atom:na + @bond:f-nh @atom:f @atom:nh + @bond:f-no @atom:f @atom:no + @bond:f-o @atom:f @atom:o + @bond:f-oh @atom:f @atom:oh + @bond:f-os @atom:f @atom:os + @bond:f-p2 @atom:f @atom:p2 + @bond:f-p3 @atom:f @atom:p3 + @bond:f-p4 @atom:f @atom:p4 + @bond:f-p5 @atom:f @atom:p5 + @bond:f-s2 @atom:f @atom:s2 + @bond:f-s @atom:f @atom:s + @bond:f-s4 @atom:f @atom:s4 + @bond:f-s6 @atom:f @atom:s6 + @bond:f-sh @atom:f @atom:sh + @bond:f-ss @atom:f @atom:ss + @bond:hn-n1 @atom:hn @atom:n1 + @bond:hn-n2 @atom:hn @atom:n2 + @bond:hn-n3 @atom:hn @atom:n3 + @bond:hn-n @atom:hn @atom:n + @bond:hn-n4 @atom:hn @atom:n4 + @bond:hn-na @atom:hn @atom:na + @bond:hn-nh @atom:hn @atom:nh + @bond:hn-no @atom:hn @atom:no + @bond:ho-o @atom:ho @atom:o + @bond:ho-oh @atom:ho @atom:oh + @bond:hp-p2 @atom:hp @atom:p2 + @bond:hp-p3 @atom:hp @atom:p3 + @bond:hp-p4 @atom:hp @atom:p4 + @bond:hp-p5 @atom:hp @atom:p5 + @bond:hs-s @atom:hs @atom:s + @bond:hs-s4 @atom:hs @atom:s4 + @bond:hs-s6 @atom:hs @atom:s6 + @bond:hs-sh @atom:hs @atom:sh + @bond:i-i @atom:i @atom:i + @bond:i-n1 @atom:i @atom:n1 + @bond:i-n2 @atom:i @atom:n2 + @bond:i-n @atom:i @atom:n + @bond:i-n3 @atom:i @atom:n3 + @bond:i-n4 @atom:i @atom:n4 + @bond:i-na @atom:i @atom:na + @bond:i-nh @atom:i @atom:nh + @bond:i-no @atom:i @atom:no + @bond:i-o @atom:i @atom:o + @bond:i-oh @atom:i @atom:oh + @bond:i-os @atom:i @atom:os + @bond:i-p2 @atom:i @atom:p2 + @bond:i-p3 @atom:i @atom:p3 + @bond:i-p4 @atom:i @atom:p4 + @bond:i-p5 @atom:i @atom:p5 + @bond:i-s @atom:i @atom:s + @bond:i-s4 @atom:i @atom:s4 + @bond:i-s6 @atom:i @atom:s6 + @bond:i-sh @atom:i @atom:sh + @bond:i-ss @atom:i @atom:ss + @bond:n1-n1 @atom:n1 @atom:n1 + @bond:n1-n2 @atom:n1 @atom:n2 + @bond:n1-n3 @atom:n1 @atom:n3 + @bond:n1-n4 @atom:n1 @atom:n4 + @bond:n1-na @atom:n1 @atom:na + @bond:n1-nc @atom:n1 @atom:nc + @bond:n1-nd @atom:n1 @atom:nd + @bond:n1-ne @atom:n1 @atom:ne + @bond:n1-nf @atom:n1 @atom:nf + @bond:n1-nh @atom:n1 @atom:nh + @bond:n1-no @atom:n1 @atom:no + @bond:n1-o @atom:n1 @atom:o + @bond:n1-oh @atom:n1 @atom:oh + @bond:n1-os @atom:n1 @atom:os + @bond:n1-p2 @atom:n1 @atom:p2 + @bond:n1-p3 @atom:n1 @atom:p3 + @bond:n1-p4 @atom:n1 @atom:p4 + @bond:n1-p5 @atom:n1 @atom:p5 + @bond:n1-s2 @atom:n1 @atom:s2 + @bond:n1-s @atom:n1 @atom:s + @bond:n1-s4 @atom:n1 @atom:s4 + @bond:n1-s6 @atom:n1 @atom:s6 + @bond:n1-sh @atom:n1 @atom:sh + @bond:n1-ss @atom:n1 @atom:ss + @bond:n2-n2 @atom:n2 @atom:n2 + @bond:n2-n3 @atom:n2 @atom:n3 + @bond:n2-n4 @atom:n2 @atom:n4 + @bond:n2-na @atom:n2 @atom:na + @bond:n2-nc @atom:n2 @atom:nc + @bond:n2-nd @atom:n2 @atom:nd + @bond:n2-ne @atom:n2 @atom:ne + @bond:n2-nf @atom:n2 @atom:nf + @bond:n2-nh @atom:n2 @atom:nh + @bond:n2-no @atom:n2 @atom:no + @bond:n2-o @atom:n2 @atom:o + @bond:n2-oh @atom:n2 @atom:oh + @bond:n2-os @atom:n2 @atom:os + @bond:n2-p2 @atom:n2 @atom:p2 + @bond:n2-p3 @atom:n2 @atom:p3 + @bond:n2-p4 @atom:n2 @atom:p4 + @bond:n2-p5 @atom:n2 @atom:p5 + @bond:n2-pe @atom:n2 @atom:pe + @bond:n2-pf @atom:n2 @atom:pf + @bond:n2-s2 @atom:n2 @atom:s2 + @bond:n2-s4 @atom:n2 @atom:s4 + @bond:n2-s @atom:n2 @atom:s + @bond:n2-s6 @atom:n2 @atom:s6 + @bond:n2-sh @atom:n2 @atom:sh + @bond:n2-ss @atom:n2 @atom:ss + @bond:n3-n3 @atom:n3 @atom:n3 + @bond:n3-n4 @atom:n3 @atom:n4 + @bond:n3-na @atom:n3 @atom:na + @bond:n3-nh @atom:n3 @atom:nh + @bond:n3-no @atom:n3 @atom:no + @bond:n3-o @atom:n3 @atom:o + @bond:n3-oh @atom:n3 @atom:oh + @bond:n3-os @atom:n3 @atom:os + @bond:n3-p2 @atom:n3 @atom:p2 + @bond:n3-p3 @atom:n3 @atom:p3 + @bond:n3-p4 @atom:n3 @atom:p4 + @bond:n3-p5 @atom:n3 @atom:p5 + @bond:n3-py @atom:n3 @atom:py + @bond:n3-s @atom:n3 @atom:s + @bond:n3-s4 @atom:n3 @atom:s4 + @bond:n3-s6 @atom:n3 @atom:s6 + @bond:n3-sh @atom:n3 @atom:sh + @bond:n3-ss @atom:n3 @atom:ss + @bond:n3-sy @atom:n3 @atom:sy + @bond:n4-n4 @atom:n4 @atom:n4 + @bond:n4-na @atom:n4 @atom:na + @bond:n4-nh @atom:n4 @atom:nh + @bond:n4-no @atom:n4 @atom:no + @bond:n4-o @atom:n4 @atom:o + @bond:n4-oh @atom:n4 @atom:oh + @bond:n4-os @atom:n4 @atom:os + @bond:n4-p2 @atom:n4 @atom:p2 + @bond:n4-p3 @atom:n4 @atom:p3 + @bond:n4-p4 @atom:n4 @atom:p4 + @bond:n4-p5 @atom:n4 @atom:p5 + @bond:n4-py @atom:n4 @atom:py + @bond:n4-s @atom:n4 @atom:s + @bond:n4-s4 @atom:n4 @atom:s4 + @bond:n4-s6 @atom:n4 @atom:s6 + @bond:n4-sh @atom:n4 @atom:sh + @bond:n4-ss @atom:n4 @atom:ss + @bond:na-na @atom:na @atom:na + @bond:na-nb @atom:na @atom:nb + @bond:na-nc @atom:na @atom:nc + @bond:na-nd @atom:na @atom:nd + @bond:na-nh @atom:na @atom:nh + @bond:na-no @atom:na @atom:no + @bond:na-o @atom:na @atom:o + @bond:na-oh @atom:na @atom:oh + @bond:na-os @atom:na @atom:os + @bond:na-p2 @atom:na @atom:p2 + @bond:na-p3 @atom:na @atom:p3 + @bond:na-p4 @atom:na @atom:p4 + @bond:na-p5 @atom:na @atom:p5 + @bond:na-pc @atom:na @atom:pc + @bond:na-pd @atom:na @atom:pd + @bond:na-py @atom:na @atom:py + @bond:na-s @atom:na @atom:s + @bond:na-s4 @atom:na @atom:s4 + @bond:na-s6 @atom:na @atom:s6 + @bond:na-sh @atom:na @atom:sh + @bond:na-ss @atom:na @atom:ss + @bond:na-sy @atom:na @atom:sy + @bond:nb-nb @atom:nb @atom:nb + @bond:nb-pb @atom:nb @atom:pb + @bond:nc-nc @atom:nc @atom:nc + @bond:nc-nd @atom:nc @atom:nd + @bond:nc-os @atom:nc @atom:os + @bond:nc-ss @atom:nc @atom:ss + @bond:nc-sy @atom:nc @atom:sy + @bond:nd-nd @atom:nd @atom:nd + @bond:nd-os @atom:nd @atom:os + @bond:nd-ss @atom:nd @atom:ss + @bond:nd-sy @atom:nd @atom:sy + @bond:ne-ne @atom:ne @atom:ne + @bond:ne-nf @atom:ne @atom:nf + @bond:ne-o @atom:ne @atom:o + @bond:ne-p2 @atom:ne @atom:p2 + @bond:ne-pe @atom:ne @atom:pe + @bond:ne-px @atom:ne @atom:px + @bond:ne-py @atom:ne @atom:py + @bond:ne-s @atom:ne @atom:s + @bond:ne-sx @atom:ne @atom:sx + @bond:ne-sy @atom:ne @atom:sy + @bond:nf-nf @atom:nf @atom:nf + @bond:nf-o @atom:nf @atom:o + @bond:nf-p2 @atom:nf @atom:p2 + @bond:nf-pf @atom:nf @atom:pf + @bond:nf-px @atom:nf @atom:px + @bond:nf-py @atom:nf @atom:py + @bond:nf-s @atom:nf @atom:s + @bond:nf-sx @atom:nf @atom:sx + @bond:nf-sy @atom:nf @atom:sy + @bond:nh-nh @atom:nh @atom:nh + @bond:nh-no @atom:nh @atom:no + @bond:nh-o @atom:nh @atom:o + @bond:nh-oh @atom:nh @atom:oh + @bond:nh-os @atom:nh @atom:os + @bond:nh-p2 @atom:nh @atom:p2 + @bond:nh-p3 @atom:nh @atom:p3 + @bond:nh-p4 @atom:nh @atom:p4 + @bond:nh-p5 @atom:nh @atom:p5 + @bond:nh-s @atom:nh @atom:s + @bond:nh-s4 @atom:nh @atom:s4 + @bond:nh-s6 @atom:nh @atom:s6 + @bond:nh-sh @atom:nh @atom:sh + @bond:nh-ss @atom:nh @atom:ss + @bond:nh-sy @atom:nh @atom:sy + @bond:n-n1 @atom:n @atom:n1 + @bond:n-n2 @atom:n @atom:n2 + @bond:n-n3 @atom:n @atom:n3 + @bond:n-n4 @atom:n @atom:n4 + @bond:n-n @atom:n @atom:n + @bond:n-na @atom:n @atom:na + @bond:n-nc @atom:n @atom:nc + @bond:n-nd @atom:n @atom:nd + @bond:n-nh @atom:n @atom:nh + @bond:n-no @atom:n @atom:no + @bond:n-o @atom:n @atom:o + @bond:n-oh @atom:n @atom:oh + @bond:no-no @atom:no @atom:no + @bond:no-o @atom:no @atom:o + @bond:no-oh @atom:no @atom:oh + @bond:no-os @atom:no @atom:os + @bond:no-os @atom:no @atom:os + @bond:no-p2 @atom:no @atom:p2 + @bond:no-p3 @atom:no @atom:p3 + @bond:no-p4 @atom:no @atom:p4 + @bond:no-p5 @atom:no @atom:p5 + @bond:no-s @atom:no @atom:s + @bond:n-os @atom:n @atom:os + @bond:no-s4 @atom:no @atom:s4 + @bond:no-s6 @atom:no @atom:s6 + @bond:no-sh @atom:no @atom:sh + @bond:no-ss @atom:no @atom:ss + @bond:n-p2 @atom:n @atom:p2 + @bond:n-p3 @atom:n @atom:p3 + @bond:n-p4 @atom:n @atom:p4 + @bond:n-p5 @atom:n @atom:p5 + @bond:n-pc @atom:n @atom:pc + @bond:n-pd @atom:n @atom:pd + @bond:n-s @atom:n @atom:s + @bond:n-s4 @atom:n @atom:s4 + @bond:n-s6 @atom:n @atom:s6 + @bond:n-sh @atom:n @atom:sh + @bond:n-ss @atom:n @atom:ss + @bond:n-sy @atom:n @atom:sy + @bond:oh-oh @atom:oh @atom:oh + @bond:oh-os @atom:oh @atom:os + @bond:oh-p2 @atom:oh @atom:p2 + @bond:oh-p3 @atom:oh @atom:p3 + @bond:oh-p4 @atom:oh @atom:p4 + @bond:oh-p5 @atom:oh @atom:p5 + @bond:oh-py @atom:oh @atom:py + @bond:oh-s @atom:oh @atom:s + @bond:oh-s4 @atom:oh @atom:s4 + @bond:oh-s6 @atom:oh @atom:s6 + @bond:oh-sh @atom:oh @atom:sh + @bond:oh-ss @atom:oh @atom:ss + @bond:oh-sy @atom:oh @atom:sy + @bond:o-o @atom:o @atom:o + @bond:o-oh @atom:o @atom:oh + @bond:o-os @atom:o @atom:os + @bond:o-p2 @atom:o @atom:p2 + @bond:o-p3 @atom:o @atom:p3 + @bond:o-p4 @atom:o @atom:p4 + @bond:o-p5 @atom:o @atom:p5 + @bond:o-pe @atom:o @atom:pe + @bond:o-pf @atom:o @atom:pf + @bond:o-px @atom:o @atom:px + @bond:o-py @atom:o @atom:py + @bond:o-s @atom:o @atom:s + @bond:o-s2 @atom:o @atom:s2 + @bond:o-s4 @atom:o @atom:s4 + @bond:o-s6 @atom:o @atom:s6 + @bond:o-sh @atom:o @atom:sh + @bond:os-os @atom:os @atom:os + @bond:os-p2 @atom:os @atom:p2 + @bond:os-p3 @atom:os @atom:p3 + @bond:os-p4 @atom:os @atom:p4 + @bond:os-p5 @atom:os @atom:p5 + @bond:os-py @atom:os @atom:py + @bond:os-s @atom:os @atom:s + @bond:o-ss @atom:o @atom:ss + @bond:os-s4 @atom:os @atom:s4 + @bond:os-s6 @atom:os @atom:s6 + @bond:os-sh @atom:os @atom:sh + @bond:os-ss @atom:os @atom:ss + @bond:os-sy @atom:os @atom:sy + @bond:o-sx @atom:o @atom:sx + @bond:o-sy @atom:o @atom:sy + @bond:p2-p2 @atom:p2 @atom:p2 + @bond:p2-p3 @atom:p2 @atom:p3 + @bond:p2-p4 @atom:p2 @atom:p4 + @bond:p2-p5 @atom:p2 @atom:p5 + @bond:p2-pe @atom:p2 @atom:pe + @bond:p2-pf @atom:p2 @atom:pf + @bond:p2-s @atom:p2 @atom:s + @bond:p2-s4 @atom:p2 @atom:s4 + @bond:p2-s6 @atom:p2 @atom:s6 + @bond:p2-sh @atom:p2 @atom:sh + @bond:p2-ss @atom:p2 @atom:ss + @bond:p3-p3 @atom:p3 @atom:p3 + @bond:p3-p4 @atom:p3 @atom:p4 + @bond:p3-p5 @atom:p3 @atom:p5 + @bond:p3-s @atom:p3 @atom:s + @bond:p3-s4 @atom:p3 @atom:s4 + @bond:p3-s6 @atom:p3 @atom:s6 + @bond:p3-sh @atom:p3 @atom:sh + @bond:p3-ss @atom:p3 @atom:ss + @bond:p4-p4 @atom:p4 @atom:p4 + @bond:p4-p5 @atom:p4 @atom:p5 + @bond:p4-s @atom:p4 @atom:s + @bond:p4-s4 @atom:p4 @atom:s4 + @bond:p4-s6 @atom:p4 @atom:s6 + @bond:p4-sh @atom:p4 @atom:sh + @bond:p4-ss @atom:p4 @atom:ss + @bond:p5-p5 @atom:p5 @atom:p5 + @bond:p5-s @atom:p5 @atom:s + @bond:p5-s4 @atom:p5 @atom:s4 + @bond:p5-s6 @atom:p5 @atom:s6 + @bond:p5-sh @atom:p5 @atom:sh + @bond:p5-ss @atom:p5 @atom:ss + @bond:pe-pe @atom:pe @atom:pe + @bond:pe-pf @atom:pe @atom:pf + @bond:pe-px @atom:pe @atom:px + @bond:pe-py @atom:pe @atom:py + @bond:pe-s @atom:pe @atom:s + @bond:pe-sx @atom:pe @atom:sx + @bond:pe-sy @atom:pe @atom:sy + @bond:pf-pf @atom:pf @atom:pf + @bond:pf-px @atom:pf @atom:px + @bond:pf-py @atom:pf @atom:py + @bond:pf-s @atom:pf @atom:s + @bond:pf-sx @atom:pf @atom:sx + @bond:pf-sy @atom:pf @atom:sy + @bond:px-py @atom:px @atom:py + @bond:px-sx @atom:px @atom:sx + @bond:px-sy @atom:px @atom:sy + @bond:py-py @atom:py @atom:py + @bond:py-sx @atom:py @atom:sx + @bond:py-sy @atom:py @atom:sy + @bond:s4-s4 @atom:s4 @atom:s4 + @bond:s4-s6 @atom:s4 @atom:s6 + @bond:s4-sh @atom:s4 @atom:sh + @bond:s4-ss @atom:s4 @atom:ss + @bond:s6-s6 @atom:s6 @atom:s6 + @bond:s6-sh @atom:s6 @atom:sh + @bond:s6-ss @atom:s6 @atom:ss + @bond:sh-sh @atom:sh @atom:sh + @bond:sh-ss @atom:sh @atom:ss + @bond:s-s @atom:s @atom:s + @bond:s-s2 @atom:s @atom:s2 + @bond:s-s4 @atom:s @atom:s4 + @bond:s-s6 @atom:s @atom:s6 + @bond:s-sh @atom:s @atom:sh + @bond:s-ss @atom:s @atom:ss + @bond:ss-ss @atom:ss @atom:ss + @bond:sx-sx @atom:sx @atom:sx + @bond:sx-sy @atom:sx @atom:sy + @bond:sy-sy @atom:sy @atom:sy + } # (end of Bonds By Type) + + write_once("In Settings") { + angle_coeff @angle:hw-ow-hw harmonic 42.730 104.520 # AMBER 1 TIP3P_water + angle_coeff @angle:hw-hw-ow harmonic 0.000 127.740 # AMBER 1 (found_in_crystallographic_water_with_3_bonds) + angle_coeff @angle:br-c1-br harmonic 57.760 180.000 # Guess 0 + angle_coeff @angle:br-c1-c1 harmonic 54.930 180.000 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-c1-c1 harmonic 64.410 180.000 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-c1-c2 harmonic 60.840 180.000 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-c1-c3 harmonic 56.280 178.460 # SOURCE4 188 0.6631 + angle_coeff @angle:c1-c1-ca harmonic 56.920 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-cl harmonic 55.270 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-f harmonic 61.020 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-ha harmonic 44.840 178.380 # SOURCE3 41 2.0683 + angle_coeff @angle:c1-c1-hc harmonic 44.730 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-i harmonic 49.800 180.000 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-c1-n1 harmonic 67.170 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-n2 harmonic 65.170 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-n3 harmonic 59.770 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-n4 harmonic 59.090 179.560 # SOURCE3 3 0.3096 + angle_coeff @angle:c1-c1-n harmonic 62.130 177.180 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-c1-na harmonic 61.230 176.750 # SOURCE3 8 2.9328 + angle_coeff @angle:c1-c1-nh harmonic 61.440 179.270 # SOURCE3 3 0.2357 + angle_coeff @angle:c1-c1-no harmonic 59.380 180.000 # SOURCE3 3 0.0000 + angle_coeff @angle:c1-c1-o harmonic 66.790 180.000 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-c1-oh harmonic 62.700 176.650 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-c1-os harmonic 62.770 176.420 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-c1-p2 harmonic 51.510 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-p3 harmonic 52.470 169.630 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-c1-p4 harmonic 50.940 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-p5 harmonic 52.560 176.170 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-c1-s4 harmonic 68.490 167.470 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-c1-s6 harmonic 68.020 174.380 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-c1-s harmonic 70.430 179.970 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-c1-sh harmonic 68.520 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-ss harmonic 69.890 173.220 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-c1-c2 harmonic 58.200 180.000 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-c1-ce harmonic 58.180 179.010 # SOURCE4 6 0.4656 + angle_coeff @angle:c2-c1-n1 harmonic 63.140 180.000 # HF/6-31G* 1 + angle_coeff @angle:c2-c1-o harmonic 63.070 179.500 # SOURCE2 1 0.0000 + angle_coeff @angle:c2-c1-s2 harmonic 71.800 172.980 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-c1-c3 harmonic 51.750 180.000 # Guess 0 + angle_coeff @angle:c3-c1-cg harmonic 55.790 178.520 # SOURCE4 39 0.5063 + angle_coeff @angle:c3-c1-n1 harmonic 58.100 178.500 # SOURCE4 77 0.5443 + angle_coeff @angle:ca-c1-ca harmonic 52.830 180.000 # Guess 0 + angle_coeff @angle:c-c1-c1 harmonic 56.330 180.000 # SOURCE3 1 + angle_coeff @angle:cg-c1-ha harmonic 43.980 177.410 # SOURCE3 22 2.4947 + angle_coeff @angle:ch-c1-ha harmonic 43.980 177.410 # SOURCE3 22 same_as_cg-c1-ha + angle_coeff @angle:cl-c1-cl harmonic 53.920 180.000 # Guess 0 + angle_coeff @angle:f-c1-f harmonic 58.190 180.000 # Guess 0 + angle_coeff @angle:i-c1-i harmonic 53.410 180.000 # Guess 0 + angle_coeff @angle:n1-c1-n1 harmonic 93.200 102.010 # SOURCE3 1 + angle_coeff @angle:n1-c1-n3 harmonic 63.710 169.700 # SOURCE2 1 0.0000 + angle_coeff @angle:n1-c1-nh harmonic 64.020 177.430 # SOURCE4 7 0.7877 + angle_coeff @angle:n1-c1-os harmonic 64.720 178.590 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-c1-p3 harmonic 53.480 171.200 # SOURCE2 1 0.0000 + angle_coeff @angle:n1-c1-ss harmonic 70.640 178.680 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-c1-n2 harmonic 65.990 180.000 # Guess 0 + angle_coeff @angle:n2-c1-o harmonic 69.150 171.790 # SOURCE3 2 0.3594 + angle_coeff @angle:n2-c1-s harmonic 72.750 176.010 # SOURCE4 9 0.1123 + angle_coeff @angle:n3-c1-n3 harmonic 57.360 180.000 # Guess 0 + angle_coeff @angle:n4-c1-n4 harmonic 56.350 180.000 # Guess 0 + angle_coeff @angle:na-c1-na harmonic 58.620 180.000 # Guess 0 + angle_coeff @angle:ne-c1-o harmonic 69.390 172.330 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-c1-s harmonic 72.880 175.810 # SOURCE4 8 0.2356 + angle_coeff @angle:nf-c1-o harmonic 69.390 172.330 # SOURCE3 1 same_as_ne-c1-o + angle_coeff @angle:nh-c1-nh harmonic 59.550 180.000 # Guess 0 + angle_coeff @angle:n-c1-n harmonic 60.030 180.000 # Guess 0 + angle_coeff @angle:no-c1-no harmonic 56.830 180.000 # Guess 0 + angle_coeff @angle:oh-c1-oh harmonic 60.910 180.000 # Guess 0 + angle_coeff @angle:o-c1-o harmonic 69.270 180.000 # Guess 0 + angle_coeff @angle:os-c1-os harmonic 60.960 180.000 # Guess 0 + angle_coeff @angle:p2-c1-p2 harmonic 50.310 180.000 # Guess 0 + angle_coeff @angle:p3-c1-p3 harmonic 49.750 180.000 # Guess 0 + angle_coeff @angle:p4-c1-p4 harmonic 49.750 180.000 # Guess 0 + angle_coeff @angle:p5-c1-p5 harmonic 50.800 180.000 # Guess 0 + angle_coeff @angle:s2-c1-s2 harmonic 89.430 180.000 # Guess 0 + angle_coeff @angle:s4-c1-s4 harmonic 81.700 180.000 # Guess 0 + angle_coeff @angle:s6-c1-s6 harmonic 82.840 180.000 # Guess 0 + angle_coeff @angle:sh-c1-sh harmonic 84.910 180.000 # Guess 0 + angle_coeff @angle:s-c1-s harmonic 87.510 180.000 # Guess 0 + angle_coeff @angle:ss-c1-ss harmonic 84.960 180.000 # Guess 0 + angle_coeff @angle:br-c2-br harmonic 68.560 115.060 # SOURCE3 1 0.0000 + angle_coeff @angle:br-c2-c2 harmonic 63.970 118.960 # SOURCE4 6 0.4902 + angle_coeff @angle:br-c2-c3 harmonic 63.710 115.330 # SOURCE4 6 0.5872 + angle_coeff @angle:br-c2-ce harmonic 63.210 121.590 # SOURCE4 7 0.7078 + angle_coeff @angle:br-c2-h4 harmonic 43.040 113.940 # SOURCE4 6 0.4017 + angle_coeff @angle:br-c2-ha harmonic 43.180 113.280 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-c2-c1 harmonic 72.260 116.770 # SOURCE3 1 + angle_coeff @angle:c1-c2-c2 harmonic 70.340 121.620 # SOURCE3 1 + angle_coeff @angle:c1-c2-c3 harmonic 64.220 124.920 # SOURCE4 17 0.7576 + angle_coeff @angle:c1-c2-f harmonic 67.990 124.900 # SOURCE2 1 0.0000 + angle_coeff @angle:c1-c2-ha harmonic 50.430 121.370 # SOURCE3 8 0.0055 + angle_coeff @angle:c2-c2-c2 harmonic 69.840 121.810 # SOURCE3 10 0.3843 + angle_coeff @angle:c2-c2-c3 harmonic 64.330 123.420 # SOURCE3 41 2.6057 + angle_coeff @angle:c2-c2-ca harmonic 66.880 117.000 # SOURCE3 1 + angle_coeff @angle:c2-c2-cc harmonic 70.220 117.210 # SOURCE3 2 0.3418 + angle_coeff @angle:c2-c2-cd harmonic 70.220 117.210 # SOURCE3 2 same_as_c2-c2-cc + angle_coeff @angle:c2-c2-cl harmonic 62.820 122.850 # SOURCE4 23 0.6711 + angle_coeff @angle:c2-c2-cx harmonic 64.500 125.400 # SOURCE4 12 1.8494 + angle_coeff @angle:c2-c2-cy harmonic 70.420 103.300 # SOURCE2 1 0.0000 + angle_coeff @angle:c2-c2-f harmonic 68.110 122.920 # SOURCE4 12 0.5301 + angle_coeff @angle:c2-c2-h4 harmonic 49.750 122.540 # SOURCE4 69 1.1900 + angle_coeff @angle:c2-c2-ha harmonic 50.040 120.940 # SOURCE3 254 1.3150 + angle_coeff @angle:c2-c2-hc harmonic 50.300 119.700 # SOURCE3 1 + angle_coeff @angle:c2-c2-hx harmonic 48.980 126.450 # SOURCE3 3 0.0219 + angle_coeff @angle:c2-c2-i harmonic 56.280 121.030 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-c2-n1 harmonic 71.690 122.980 # HF/6-31G* 1 + angle_coeff @angle:c2-c2-n2 harmonic 71.290 126.010 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-c2-n3 harmonic 70.330 124.550 # SOURCE3 1 + angle_coeff @angle:c2-c2-n4 harmonic 67.180 121.520 # SOURCE3 5 1.2656 + angle_coeff @angle:c2-c2-n harmonic 68.860 123.200 # SOURCE4 15 1.8657 + angle_coeff @angle:c2-c2-na harmonic 69.830 121.380 # SOURCE3 26 6.9463 + angle_coeff @angle:c2-c2-nh harmonic 69.800 124.990 # SOURCE3 7 0.9929 + angle_coeff @angle:c2-c2-no harmonic 67.520 124.090 # SOURCE4 6 1.2772 + angle_coeff @angle:c2-c2-o harmonic 71.920 130.890 # SOURCE3 2 0.0201 + angle_coeff @angle:c2-c2-oh harmonic 71.640 122.070 # SOURCE4 6 1.0883 + angle_coeff @angle:c2-c2-os harmonic 71.040 121.890 # SOURCE4 33 1.3457 + angle_coeff @angle:c2-c2-p2 harmonic 66.940 115.100 # SOURCE3 1 + angle_coeff @angle:c2-c2-p3 harmonic 59.410 124.830 # SOURCE3 5 2.1222 + angle_coeff @angle:c2-c2-p4 harmonic 61.010 119.760 # SOURCE3 1 + angle_coeff @angle:c2-c2-p5 harmonic 58.230 125.970 # SOURCE3 1 + angle_coeff @angle:c2-c2-s4 harmonic 79.550 119.840 # SOURCE3 1 + angle_coeff @angle:c2-c2-s6 harmonic 79.490 120.010 # SOURCE3 1 + angle_coeff @angle:c2-c2-s harmonic 77.520 129.370 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-c2-sh harmonic 77.030 125.700 # SOURCE3 3 1.3390 + angle_coeff @angle:c2-c2-ss harmonic 79.470 122.860 # SOURCE4 13 1.7467 + angle_coeff @angle:c3-c2-c3 harmonic 62.700 116.520 # SOURCE3 15 3.1001 + angle_coeff @angle:c3-c2-cc harmonic 63.220 125.380 # SOURCE4 26 1.8978 + angle_coeff @angle:c3-c2-cd harmonic 63.160 125.640 # SOURCE3 1 same_as_c3-c2-cc + angle_coeff @angle:c3-c2-ce harmonic 64.190 123.020 # SOURCE4 1189 1.9006 + angle_coeff @angle:c3-c2-cf harmonic 63.960 123.870 # SOURCE4 99 1.2875 + angle_coeff @angle:c3-c2-h4 harmonic 45.300 119.250 # SOURCE4 22 2.1707 + angle_coeff @angle:c3-c2-ha harmonic 45.660 117.300 # SOURCE3 33 1.7453 + angle_coeff @angle:c3-c2-hc harmonic 45.150 120.000 # SOURCE3 1 + angle_coeff @angle:c3-c2-n2 harmonic 66.470 123.520 # SOURCE4 141 2.2935 + angle_coeff @angle:c3-c2-n harmonic 66.790 114.800 # SOURCE4 12 1.8112 + angle_coeff @angle:c3-c2-na harmonic 64.950 122.540 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-c2-ne harmonic 66.960 122.150 # SOURCE3 4 0.2197 + angle_coeff @angle:c3-c2-nf harmonic 66.960 122.150 # SOURCE3 4 same_as_c3-c2-ne + angle_coeff @angle:c3-c2-nh harmonic 66.690 118.590 # SOURCE3 6 2.2622 + angle_coeff @angle:c3-c2-o harmonic 67.880 123.180 # SOURCE4 5 0.9226 + angle_coeff @angle:c3-c2-oh harmonic 68.500 115.040 # SOURCE4 36 2.0110 + angle_coeff @angle:c3-c2-os harmonic 68.770 112.690 # SOURCE4 50 2.4254 + angle_coeff @angle:c3-c2-p2 harmonic 62.400 122.740 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-c2-s harmonic 79.470 115.440 # SOURCE3 2 0.0115 + angle_coeff @angle:c3-c2-ss harmonic 77.990 119.660 # SOURCE4 45 1.9732 + angle_coeff @angle:ca-c2-ca harmonic 63.510 117.880 # SOURCE3 1 + angle_coeff @angle:ca-c2-hc harmonic 45.280 123.300 # SOURCE3 1 + angle_coeff @angle:c-c2-c2 harmonic 67.930 120.700 # SOURCE3 1 + angle_coeff @angle:c-c2-c3 harmonic 63.870 119.700 # SOURCE3 1 + angle_coeff @angle:c-c2-c harmonic 66.570 118.880 # SOURCE3 1 + angle_coeff @angle:cc-c2-h4 harmonic 49.190 120.330 # SOURCE4 7 0.0865 + angle_coeff @angle:cc-c2-ha harmonic 49.070 120.760 # SOURCE3 11 1.4155 + angle_coeff @angle:cc-c2-nh harmonic 69.460 122.960 # SOURCE4 10 0.7347 + angle_coeff @angle:cc-c2-o harmonic 72.800 123.590 # SOURCE4 6 0.0560 + angle_coeff @angle:cd-c2-ha harmonic 49.070 120.760 # SOURCE3 11 1.4155 + angle_coeff @angle:ce-c2-cl harmonic 62.430 123.900 # SOURCE4 11 0.3570 + angle_coeff @angle:ce-c2-h4 harmonic 49.380 122.290 # SOURCE4 75 1.4008 + angle_coeff @angle:ce-c2-ha harmonic 49.570 121.190 # SOURCE3 122 0.5318 + angle_coeff @angle:ce-c2-na harmonic 68.820 123.710 # SOURCE4 6 2.0109 + angle_coeff @angle:ce-c2-nh harmonic 70.640 120.720 # SOURCE4 93 2.2537 + angle_coeff @angle:ce-c2-no harmonic 68.450 119.650 # SOURCE4 5 0.9817 + angle_coeff @angle:ce-c2-o harmonic 73.660 123.080 # SOURCE4 5 0.2391 + angle_coeff @angle:ce-c2-oh harmonic 70.900 123.270 # SOURCE4 42 1.8111 + angle_coeff @angle:ce-c2-os harmonic 70.470 122.520 # SOURCE4 51 2.4680 + angle_coeff @angle:cf-c2-ha harmonic 49.570 121.190 # SOURCE3 122 same_as_ce-c2-ha + angle_coeff @angle:c-c2-ha harmonic 47.670 121.330 # SOURCE3 4 0.2462 + angle_coeff @angle:c-c2-hc harmonic 48.000 119.700 # SOURCE3 1 + angle_coeff @angle:cl-c2-cl harmonic 64.100 114.270 # SOURCE4 10 0.5850 + angle_coeff @angle:cl-c2-h4 harmonic 43.820 113.770 # SOURCE4 9 0.6228 + angle_coeff @angle:cl-c2-ha harmonic 43.940 113.200 # SOURCE3 1 0.0000 + angle_coeff @angle:cx-c2-ha harmonic 46.610 115.890 # SOURCE4 15 0.3682 + angle_coeff @angle:f-c2-f harmonic 70.670 109.600 # SOURCE2 2 0.6000 + angle_coeff @angle:f-c2-ha harmonic 51.250 110.000 # SOURCE2 1 0.0000 + angle_coeff @angle:h4-c2-n2 harmonic 52.400 120.690 # SOURCE4 13 1.3105 + angle_coeff @angle:h4-c2-n harmonic 50.480 113.570 # SOURCE4 26 1.0283 + angle_coeff @angle:h4-c2-na harmonic 51.030 113.220 # SOURCE4 9 0.6345 + angle_coeff @angle:h4-c2-ne harmonic 52.870 119.630 # SOURCE4 10 1.6786 + angle_coeff @angle:h4-c2-nh harmonic 51.550 115.640 # SOURCE4 31 1.0081 + angle_coeff @angle:h4-c2-no harmonic 49.390 113.380 # SOURCE4 6 0.1240 + angle_coeff @angle:h4-c2-os harmonic 52.230 113.700 # SOURCE3 13 2.0464 + angle_coeff @angle:h4-c2-ss harmonic 54.230 118.470 # SOURCE3 9 2.5335 + angle_coeff @angle:h5-c2-n2 harmonic 52.410 120.160 # SOURCE4 27 1.8999 + angle_coeff @angle:h5-c2-na harmonic 48.230 126.390 # SOURCE3 4 0.3299 + angle_coeff @angle:h5-c2-ne harmonic 52.760 119.620 # SOURCE4 17 1.3235 + angle_coeff @angle:h5-c2-nh harmonic 51.850 113.930 # SOURCE4 50 0.8394 + angle_coeff @angle:ha-c2-ha harmonic 38.020 117.650 # SOURCE3 349 1.3426 + angle_coeff @angle:ha-c2-n1 harmonic 51.830 120.760 # SOURCE3 8 0.6632 + angle_coeff @angle:ha-c2-n2 harmonic 52.390 120.540 # SOURCE3 92 1.4571 + angle_coeff @angle:ha-c2-n3 harmonic 52.440 113.540 # SOURCE3 1 + angle_coeff @angle:ha-c2-n harmonic 50.490 113.400 # SOURCE3 4 1.2182 + angle_coeff @angle:ha-c2-na harmonic 51.180 112.420 # SOURCE3 8 0.6507 + angle_coeff @angle:ha-c2-ne harmonic 52.480 121.180 # SOURCE3 68 0.6824 + angle_coeff @angle:ha-c2-nf harmonic 52.480 121.180 # SOURCE3 68 same_as_ha-c2-ne + angle_coeff @angle:ha-c2-nh harmonic 51.290 116.680 # SOURCE3 13 2.5734 + angle_coeff @angle:ha-c2-no harmonic 49.640 112.140 # SOURCE3 2 0.0264 + angle_coeff @angle:ha-c2-o harmonic 55.300 117.230 # SOURCE3 2 0.0201 + angle_coeff @angle:ha-c2-oh harmonic 52.340 116.180 # SOURCE3 2 0.0000 + angle_coeff @angle:ha-c2-os harmonic 52.430 112.690 # SOURCE3 13 2.5851 + angle_coeff @angle:ha-c2-p2 harmonic 44.050 121.480 # SOURCE3 122 0.4329 + angle_coeff @angle:ha-c2-p3 harmonic 41.120 114.310 # SOURCE3 3 0.0000 + angle_coeff @angle:ha-c2-p4 harmonic 40.790 117.860 # SOURCE3 1 + angle_coeff @angle:ha-c2-p5 harmonic 39.360 120.100 # SOURCE3 2 0.0000 + angle_coeff @angle:ha-c2-pe harmonic 43.490 121.460 # SOURCE3 104 0.7821 + angle_coeff @angle:ha-c2-pf harmonic 43.490 121.460 # SOURCE3 104 same_as_ha-c2-pe + angle_coeff @angle:ha-c2-s2 harmonic 58.460 118.740 # SOURCE3 2 0.0000 + angle_coeff @angle:ha-c2-s4 harmonic 54.190 115.300 # SOURCE3 2 0.0000 + angle_coeff @angle:ha-c2-s harmonic 54.950 115.700 # SOURCE3 2 0.0000 + angle_coeff @angle:ha-c2-s6 harmonic 53.880 116.600 # SOURCE3 2 0.0000 + angle_coeff @angle:ha-c2-sh harmonic 54.480 111.740 # SOURCE3 1 0.0000 + angle_coeff @angle:ha-c2-ss harmonic 54.640 116.720 # SOURCE3 7 2.7543 + angle_coeff @angle:hc-c2-hc harmonic 37.810 118.920 # SOURCE3 1 + angle_coeff @angle:hc-c2-n2 harmonic 52.420 120.400 # SOURCE3 1 + angle_coeff @angle:hc-c2-n harmonic 50.350 114.040 # SOURCE3 1 + angle_coeff @angle:hc-c2-na harmonic 49.730 119.100 # SOURCE3 1 + angle_coeff @angle:hc-c2-nh harmonic 52.030 113.360 # SOURCE3 1 + angle_coeff @angle:hc-c2-no harmonic 49.640 112.120 # SOURCE3 1 + angle_coeff @angle:hc-c2-oh harmonic 52.330 116.220 # SOURCE3 1 + angle_coeff @angle:hc-c2-os harmonic 51.650 116.110 # SOURCE3 1 + angle_coeff @angle:hc-c2-p3 harmonic 40.610 117.190 # SOURCE3 1 + angle_coeff @angle:hc-c2-p5 harmonic 39.440 119.580 # SOURCE3 1 + angle_coeff @angle:hc-c2-s4 harmonic 54.000 116.120 # SOURCE3 1 + angle_coeff @angle:hc-c2-s6 harmonic 54.150 115.450 # SOURCE3 1 + angle_coeff @angle:hc-c2-sh harmonic 53.550 115.630 # SOURCE3 1 + angle_coeff @angle:hc-c2-ss harmonic 54.900 115.620 # SOURCE3 1 + angle_coeff @angle:hx-c2-n4 harmonic 48.420 113.030 # SOURCE3 3 0.3873 + angle_coeff @angle:i-c2-i harmonic 60.960 117.940 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-c2-n1 harmonic 73.610 124.150 # HF/6-31G* 1 + angle_coeff @angle:n2-c2-n2 harmonic 77.960 113.820 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-c2-n4 harmonic 72.030 113.050 # SOURCE4 6 0.3318 + angle_coeff @angle:n2-c2-na harmonic 71.710 123.620 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-c2-nh harmonic 72.620 124.270 # SOURCE3 12 2.4114 + angle_coeff @angle:n2-c2-oh harmonic 74.360 122.080 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-c2-os harmonic 74.320 119.820 # SOURCE4 20 1.2664 + angle_coeff @angle:n2-c2-ss harmonic 79.560 129.770 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-c2-n3 harmonic 73.450 118.470 # SOURCE3 1 + angle_coeff @angle:n4-c2-n4 harmonic 67.720 113.930 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-c2-ss harmonic 81.510 116.260 # SOURCE4 7 2.4226 + angle_coeff @angle:na-c2-na harmonic 73.650 109.330 # SOURCE3 3 3.0187 + angle_coeff @angle:ne-c2-nh harmonic 73.020 123.570 # SOURCE4 126 2.4468 + angle_coeff @angle:ne-c2-os harmonic 74.860 118.760 # SOURCE4 5 0.3382 + angle_coeff @angle:ne-c2-ss harmonic 82.780 120.060 # SOURCE4 9 1.3423 + angle_coeff @angle:nf-c2-nh harmonic 73.280 122.720 # SOURCE3 2 same_as_ne-c2-nh + angle_coeff @angle:nh-c2-nh harmonic 74.460 112.720 # SOURCE4 257 1.8176 + angle_coeff @angle:nh-c2-oh harmonic 74.050 117.160 # SOURCE4 7 0.8698 + angle_coeff @angle:nh-c2-os harmonic 74.320 114.290 # SOURCE4 18 1.0900 + angle_coeff @angle:nh-c2-ss harmonic 85.090 111.550 # SOURCE4 37 1.1778 + angle_coeff @angle:n-c2-n2 harmonic 70.560 125.950 # SOURCE3 2 5.0202 + angle_coeff @angle:n-c2-n harmonic 71.550 113.230 # SOURCE3 1 0.0000 + angle_coeff @angle:n-c2-na harmonic 74.570 105.420 # SOURCE3 1 0.0000 + angle_coeff @angle:n-c2-ne harmonic 70.890 125.380 # SOURCE4 10 1.6819 + angle_coeff @angle:n-c2-nh harmonic 74.200 109.140 # SOURCE4 22 1.5634 + angle_coeff @angle:no-c2-no harmonic 69.430 113.900 # SOURCE3 1 0.0000 + angle_coeff @angle:n-c2-ss harmonic 84.580 111.060 # SOURCE4 9 0.5522 + angle_coeff @angle:oh-c2-oh harmonic 76.030 114.330 # SOURCE3 1 0.0000 + angle_coeff @angle:o-c2-o harmonic 80.230 121.690 # SOURCE3 1 + angle_coeff @angle:o-c2-oh harmonic 76.690 121.230 # SOURCE4 6 0.0958 + angle_coeff @angle:o-c2-s harmonic 81.200 127.680 # SOURCE3 2 0.0547 + angle_coeff @angle:os-c2-os harmonic 74.210 115.800 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-c2-p2 harmonic 62.800 129.800 # SOURCE3 1 + angle_coeff @angle:p3-c2-p3 harmonic 60.610 115.540 # SOURCE3 1 0.0000 + angle_coeff @angle:p5-c2-p5 harmonic 58.010 121.850 # SOURCE3 1 + angle_coeff @angle:s4-c2-s4 harmonic 99.130 120.320 # SOURCE3 1 + angle_coeff @angle:s4-c2-s6 harmonic 99.290 119.950 # SOURCE3 1 + angle_coeff @angle:s6-c2-s6 harmonic 99.280 119.970 # SOURCE3 1 + angle_coeff @angle:sh-c2-sh harmonic 102.460 110.480 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-c2-ss harmonic 100.350 117.820 # SOURCE3 1 + angle_coeff @angle:s-c2-s harmonic 100.060 121.670 # SOURCE3 1 + angle_coeff @angle:ss-c2-ss harmonic 100.540 120.240 # SOURCE3 1 0.0000 + angle_coeff @angle:br-c3-br harmonic 67.460 109.030 # SOURCE4 6 0.5435 + angle_coeff @angle:br-c3-c1 harmonic 62.770 111.800 # SOURCE2 3 0.2160 + angle_coeff @angle:br-c3-c3 harmonic 63.030 109.250 # SOURCE3 10 0.5685 + angle_coeff @angle:br-c3-c harmonic 62.920 110.370 # SOURCE4 13 2.4747 + angle_coeff @angle:br-c3-h1 harmonic 43.120 103.040 # SOURCE3 5 0.3092 + angle_coeff @angle:br-c3-h2 harmonic 42.340 107.100 # SOURCE4 7 0.2378 + angle_coeff @angle:br-c3-hc harmonic 42.400 106.500 # SOURCE3 1 + angle_coeff @angle:c1-c3-c1 harmonic 66.500 109.000 # SOURCE2 1 0.0000 + angle_coeff @angle:c1-c3-c2 harmonic 65.000 111.110 # SOURCE4 12 0.7366 + angle_coeff @angle:c1-c3-c3 harmonic 64.290 111.420 # SOURCE4 197 1.2106 + angle_coeff @angle:c1-c3-ca harmonic 64.930 110.950 # SOURCE4 28 1.1203 + angle_coeff @angle:c1-c3-cc harmonic 64.290 114.290 # SOURCE4 8 0.1535 + angle_coeff @angle:c1-c3-cd harmonic 64.360 114.060 # SOURCE4 5 0.0462 + angle_coeff @angle:c1-c3-cl harmonic 62.890 110.630 # SOURCE2 3 1.2257 + angle_coeff @angle:c1-c3-h1 harmonic 48.350 109.290 # SOURCE4 133 0.5701 + angle_coeff @angle:c1-c3-hc harmonic 48.250 109.750 # SOURCE3 12 0.8436 + angle_coeff @angle:c1-c3-hx harmonic 47.760 112.050 # SOURCE4 17 0.2587 + angle_coeff @angle:c1-c3-n3 harmonic 67.030 112.590 # SOURCE4 28 0.9555 + angle_coeff @angle:c1-c3-n4 harmonic 66.530 112.040 # SOURCE4 11 0.5701 + angle_coeff @angle:c1-c3-n harmonic 67.410 112.080 # SOURCE4 18 0.9568 + angle_coeff @angle:c1-c3-nh harmonic 67.250 112.790 # SOURCE4 8 0.9453 + angle_coeff @angle:c1-c3-oh harmonic 69.490 109.140 # SOURCE4 39 0.6500 + angle_coeff @angle:c1-c3-os harmonic 69.270 108.880 # SOURCE4 31 0.9597 + angle_coeff @angle:c2-c3-c2 harmonic 63.930 112.080 # SOURCE4 153 0.7742 + angle_coeff @angle:c2-c3-c3 harmonic 63.530 111.440 # SOURCE4 2891 1.7167 + angle_coeff @angle:c2-c3-ca harmonic 63.710 112.450 # SOURCE4 141 1.6755 + angle_coeff @angle:c2-c3-cc harmonic 64.000 112.490 # SOURCE4 15 1.7250 + angle_coeff @angle:c2-c3-cd harmonic 64.460 110.890 # SOURCE4 17 2.1339 + angle_coeff @angle:c2-c3-ce harmonic 64.080 111.750 # SOURCE4 28 1.5646 + angle_coeff @angle:c2-c3-cf harmonic 63.960 112.190 # SOURCE4 10 2.4554 + angle_coeff @angle:c2-c3-cl harmonic 62.050 112.070 # SOURCE4 6 0.9936 + angle_coeff @angle:c2-c3-cx harmonic 63.650 112.620 # SOURCE4 17 1.3287 + angle_coeff @angle:c2-c3-cy harmonic 66.760 101.330 # SOURCE4 58 0.9262 + angle_coeff @angle:c2-c3-f harmonic 66.520 110.960 # SOURCE4 25 0.2829 + angle_coeff @angle:c2-c3-h1 harmonic 47.030 110.460 # SOURCE3 17 1.1525 + angle_coeff @angle:c2-c3-h2 harmonic 46.840 111.190 # SOURCE4 17 0.8311 + angle_coeff @angle:c2-c3-hc harmonic 47.030 110.490 # SOURCE3 159 0.7479 + angle_coeff @angle:c2-c3-hx harmonic 46.830 111.450 # SOURCE4 20 0.9004 + angle_coeff @angle:c2-c3-n2 harmonic 67.090 108.990 # SOURCE4 10 1.2025 + angle_coeff @angle:c2-c3-n3 harmonic 66.470 111.520 # SOURCE4 158 1.4012 + angle_coeff @angle:c2-c3-n harmonic 66.730 111.380 # SOURCE4 67 1.7559 + angle_coeff @angle:c2-c3-na harmonic 66.240 113.300 # SOURCE4 27 1.2945 + angle_coeff @angle:c2-c3-nh harmonic 67.100 110.270 # SOURCE4 56 1.8018 + angle_coeff @angle:c2-c3-oh harmonic 68.180 110.210 # SOURCE4 220 1.4197 + angle_coeff @angle:c2-c3-os harmonic 68.450 108.480 # SOURCE4 204 1.6082 + angle_coeff @angle:c2-c3-s4 harmonic 79.190 109.730 # SOURCE4 6 0.1722 + angle_coeff @angle:c2-c3-ss harmonic 80.520 104.970 # SOURCE3 2 2.2248 + angle_coeff @angle:c3-c3-c3 harmonic 63.210 110.630 # SOURCE3 507 2.7845 + angle_coeff @angle:c3-c3-ca harmonic 63.250 112.090 # SOURCE4 3859 1.5523 + angle_coeff @angle:c3-c3-cc harmonic 63.570 111.920 # SOURCE4 695 1.6368 + angle_coeff @angle:c3-c3-cd harmonic 64.690 108.100 # SOURCE3 5 same_as_c3-c3-cc + angle_coeff @angle:c3-c3-ce harmonic 63.650 111.220 # SOURCE4 395 1.7751 + angle_coeff @angle:c3-c3-cf harmonic 63.900 110.370 # SOURCE4 95 1.5467 + angle_coeff @angle:c3-c3-cl harmonic 62.200 110.330 # SOURCE3 20 1.1495 + angle_coeff @angle:c3-c3-cx harmonic 63.300 111.820 # SOURCE4 179 2.4814 + angle_coeff @angle:c3-c3-cy harmonic 63.630 109.620 # SOURCE3 5 2.0747 + angle_coeff @angle:c3-c3-f harmonic 66.220 109.410 # SOURCE3 18 1.1878 + angle_coeff @angle:c3-c3-h1 harmonic 46.360 110.070 # SOURCE3 457 1.1542 + angle_coeff @angle:c3-c3-h2 harmonic 46.020 111.590 # SOURCE3 8 1.1217 + angle_coeff @angle:c3-c3-hc harmonic 46.370 110.050 # SOURCE3 2092 0.6991 + angle_coeff @angle:c3-c3-hx harmonic 46.020 111.740 # SOURCE3 15 1.2365 + angle_coeff @angle:c3-c3-i harmonic 58.480 110.960 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-c3-n1 harmonic 66.640 108.860 # SOURCE4 9 0.8093 + angle_coeff @angle:c3-c3-n2 harmonic 66.400 109.160 # SOURCE3 8 1.4079 + angle_coeff @angle:c3-c3-n3 harmonic 66.180 110.380 # SOURCE3 69 2.9054 + angle_coeff @angle:c3-c3-n4 harmonic 64.450 114.320 # SOURCE4 567 2.4412 + angle_coeff @angle:c3-c3-n harmonic 65.850 112.130 # SOURCE3 31 2.0700 + angle_coeff @angle:c3-c3-na harmonic 65.730 112.810 # SOURCE4 595 1.5050 + angle_coeff @angle:c3-c3-nh harmonic 66.390 110.450 # SOURCE4 1514 1.3881 + angle_coeff @angle:c3-c3-no harmonic 65.210 109.270 # SOURCE4 25 1.1817 + angle_coeff @angle:c3-c3-o harmonic 68.590 112.970 # SOURCE4 14 1.0277 + angle_coeff @angle:c3-c3-oh harmonic 67.720 109.430 # SOURCE3 48 1.5023 + angle_coeff @angle:c3-c3-os harmonic 67.780 108.420 # SOURCE3 122 1.6759 + angle_coeff @angle:c3-c3-p3 harmonic 60.410 113.190 # SOURCE4 15 0.2974 + angle_coeff @angle:c3-c3-p5 harmonic 61.390 112.320 # SOURCE4 106 1.1753 + angle_coeff @angle:c3-c3-s4 harmonic 78.670 110.070 # SOURCE4 38 0.8510 + angle_coeff @angle:c3-c3-s6 harmonic 79.700 110.000 # SOURCE4 152 1.4278 + angle_coeff @angle:c3-c3-sh harmonic 77.180 113.020 # SOURCE4 80 1.3442 + angle_coeff @angle:c3-c3-ss harmonic 77.330 112.690 # SOURCE3 24 2.1842 + angle_coeff @angle:c3-c3-sy harmonic 79.490 109.910 # SOURCE4 22 0.9248 + angle_coeff @angle:ca-c3-ca harmonic 63.660 112.260 # SOURCE4 385 1.7047 + angle_coeff @angle:ca-c3-cc harmonic 63.760 112.940 # SOURCE4 61 1.2579 + angle_coeff @angle:ca-c3-cd harmonic 65.180 108.080 # SOURCE3 8 same_as_ca-c3-cc + angle_coeff @angle:ca-c3-ce harmonic 63.810 112.330 # SOURCE4 51 1.1929 + angle_coeff @angle:ca-c3-cl harmonic 62.200 111.310 # SOURCE4 16 0.8077 + angle_coeff @angle:ca-c3-cx harmonic 63.690 112.100 # SOURCE4 5 2.1117 + angle_coeff @angle:ca-c3-f harmonic 66.140 111.760 # SOURCE4 449 0.3492 + angle_coeff @angle:ca-c3-h1 harmonic 46.780 110.950 # SOURCE3 12 1.1170 + angle_coeff @angle:ca-c3-h2 harmonic 47.030 109.660 # SOURCE4 29 1.2184 + angle_coeff @angle:ca-c3-hc harmonic 46.960 110.150 # SOURCE3 47 1.2602 + angle_coeff @angle:ca-c3-hx harmonic 46.690 111.440 # SOURCE4 33 0.4691 + angle_coeff @angle:ca-c3-n2 harmonic 65.920 112.490 # SOURCE4 22 1.1043 + angle_coeff @angle:ca-c3-n3 harmonic 66.180 112.130 # SOURCE4 387 1.2309 + angle_coeff @angle:ca-c3-n4 harmonic 64.870 114.540 # SOURCE4 22 2.3986 + angle_coeff @angle:ca-c3-n harmonic 66.290 112.430 # SOURCE4 201 1.5133 + angle_coeff @angle:ca-c3-na harmonic 66.270 112.810 # SOURCE4 104 1.5807 + angle_coeff @angle:ca-c3-nc harmonic 68.200 106.510 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-c3-nd harmonic 68.200 106.510 # SOURCE3 1 same_as_ca-c3-nc + angle_coeff @angle:ca-c3-nh harmonic 66.640 111.410 # SOURCE4 147 1.0074 + angle_coeff @angle:ca-c3-oh harmonic 67.940 110.550 # SOURCE4 348 1.2310 + angle_coeff @angle:ca-c3-os harmonic 68.190 108.890 # SOURCE4 411 1.0102 + angle_coeff @angle:ca-c3-p5 harmonic 61.350 113.410 # SOURCE4 19 1.4444 + angle_coeff @angle:ca-c3-s6 harmonic 79.570 111.360 # SOURCE4 15 1.4775 + angle_coeff @angle:ca-c3-ss harmonic 78.350 110.660 # SOURCE4 78 1.4797 + angle_coeff @angle:ca-c3-sx harmonic 78.680 110.800 # SOURCE4 16 0.5396 + angle_coeff @angle:c-c3-c1 harmonic 64.560 112.640 # SOURCE4 11 1.0678 + angle_coeff @angle:c-c3-c2 harmonic 64.140 111.320 # SOURCE4 92 1.8522 + angle_coeff @angle:c-c3-c3 harmonic 63.790 110.530 # SOURCE3 62 1.9636 + angle_coeff @angle:c-c3-c harmonic 64.060 111.610 # SOURCE4 151 2.1872 + angle_coeff @angle:c-c3-ca harmonic 64.130 110.990 # SOURCE4 481 1.7257 + angle_coeff @angle:c-c3-cc harmonic 63.940 112.690 # SOURCE4 61 1.4162 + angle_coeff @angle:cc-c3-cc harmonic 63.640 114.440 # SOURCE4 9 0.7894 + angle_coeff @angle:cc-c3-cd harmonic 67.300 102.350 # SOURCE3 1 0.0000 + angle_coeff @angle:cc-c3-cx harmonic 63.850 112.550 # SOURCE4 5 1.4317 + angle_coeff @angle:c-c3-cd harmonic 63.810 113.170 # SOURCE4 43 1.3583 + angle_coeff @angle:c-c3-ce harmonic 64.020 111.980 # SOURCE4 16 2.1388 + angle_coeff @angle:cc-c3-f harmonic 66.730 111.130 # SOURCE4 60 0.4791 + angle_coeff @angle:cc-c3-h1 harmonic 47.030 111.620 # SOURCE3 20 1.0215 + angle_coeff @angle:cc-c3-hc harmonic 47.200 110.860 # SOURCE3 85 1.0276 + angle_coeff @angle:cc-c3-hx harmonic 47.170 111.020 # SOURCE4 9 0.7503 + angle_coeff @angle:c-c3-cl harmonic 62.300 111.160 # SOURCE4 41 1.2257 + angle_coeff @angle:cc-c3-n2 harmonic 66.850 110.470 # SOURCE4 11 0.5153 + angle_coeff @angle:cc-c3-n3 harmonic 66.670 111.570 # SOURCE4 66 1.2287 + angle_coeff @angle:cc-c3-n4 harmonic 64.880 115.580 # SOURCE4 6 1.1723 + angle_coeff @angle:cc-c3-n harmonic 66.740 112.050 # SOURCE4 23 1.5593 + angle_coeff @angle:cc-c3-na harmonic 66.430 113.390 # SOURCE4 8 0.8010 + angle_coeff @angle:cc-c3-nc harmonic 68.370 107.040 # SOURCE3 2 0.0000 + angle_coeff @angle:cc-c3-nh harmonic 66.500 113.020 # SOURCE4 14 1.6083 + angle_coeff @angle:cc-c3-oh harmonic 68.010 111.510 # SOURCE4 61 1.4663 + angle_coeff @angle:cc-c3-os harmonic 68.570 108.820 # SOURCE4 84 1.2451 + angle_coeff @angle:cc-c3-p5 harmonic 60.750 116.230 # SOURCE4 6 0.7766 + angle_coeff @angle:cc-c3-sh harmonic 77.340 114.020 # SOURCE3 1 same_as_cd-c3-sh + angle_coeff @angle:cc-c3-ss harmonic 78.390 111.090 # SOURCE4 35 0.8623 + angle_coeff @angle:c-c3-cx harmonic 64.080 111.090 # SOURCE4 9 1.2357 + angle_coeff @angle:cd-c3-cd harmonic 65.520 107.990 # SOURCE3 10 5.1937 + angle_coeff @angle:cd-c3-f harmonic 66.530 111.800 # SOURCE4 9 0.4528 + angle_coeff @angle:cd-c3-h1 harmonic 47.030 111.620 # SOURCE3 20 1.0215 + angle_coeff @angle:cd-c3-hc harmonic 47.200 110.860 # SOURCE3 85 1.0276 + angle_coeff @angle:cd-c3-n3 harmonic 66.960 110.590 # SOURCE4 45 1.4707 + angle_coeff @angle:cd-c3-n harmonic 67.110 110.830 # SOURCE4 9 1.3462 + angle_coeff @angle:cd-c3-nd harmonic 68.370 107.040 # SOURCE3 2 same_as_cc-c3-nc + angle_coeff @angle:cd-c3-nh harmonic 67.060 111.110 # SOURCE4 7 2.0959 + angle_coeff @angle:cd-c3-oh harmonic 68.280 110.640 # SOURCE4 55 1.5008 + angle_coeff @angle:cd-c3-os harmonic 67.810 111.280 # SOURCE3 7 same_as_cc-c3-os + angle_coeff @angle:cd-c3-sh harmonic 77.340 114.020 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-c3-ss harmonic 78.450 110.910 # SOURCE4 8 0.8705 + angle_coeff @angle:ce-c3-ce harmonic 64.240 111.440 # SOURCE4 18 0.3695 + angle_coeff @angle:ce-c3-cy harmonic 66.340 102.820 # SOURCE4 6 0.1191 + angle_coeff @angle:ce-c3-h1 harmonic 47.280 109.650 # SOURCE4 98 0.9337 + angle_coeff @angle:ce-c3-hc harmonic 47.000 110.980 # SOURCE3 27 0.1559 + angle_coeff @angle:ce-c3-n3 harmonic 66.430 111.900 # SOURCE4 20 0.5035 + angle_coeff @angle:ce-c3-n harmonic 67.090 110.410 # SOURCE4 6 1.1405 + angle_coeff @angle:ce-c3-oh harmonic 68.000 111.050 # SOURCE4 17 1.5159 + angle_coeff @angle:ce-c3-os harmonic 68.640 108.100 # SOURCE4 16 1.9583 + angle_coeff @angle:ce-c3-ss harmonic 78.300 111.100 # SOURCE4 7 2.0156 + angle_coeff @angle:c-c3-f harmonic 66.820 109.980 # SOURCE4 38 0.9895 + angle_coeff @angle:cf-c3-cy harmonic 66.330 102.850 # SOURCE4 49 0.2818 + angle_coeff @angle:cf-c3-h1 harmonic 47.350 109.340 # SOURCE4 21 0.7788 + angle_coeff @angle:cf-c3-hc harmonic 47.000 110.980 # SOURCE3 27 same_as_ce-c3-hc + angle_coeff @angle:cf-c3-n3 harmonic 66.510 111.640 # SOURCE4 8 1.1575 + angle_coeff @angle:c-c3-h1 harmonic 47.630 107.660 # SOURCE3 66 1.4015 + angle_coeff @angle:c-c3-h2 harmonic 47.160 109.690 # SOURCE4 38 1.0614 + angle_coeff @angle:c-c3-hc harmonic 47.200 109.680 # SOURCE3 614 0.6426 + angle_coeff @angle:c-c3-hx harmonic 47.230 109.540 # SOURCE4 47 0.6627 + angle_coeff @angle:cl-c3-cl harmonic 62.700 111.030 # SOURCE2 6 1.1324 + angle_coeff @angle:cl-c3-f harmonic 63.600 109.020 # SOURCE4 15 0.3609 + angle_coeff @angle:cl-c3-h1 harmonic 43.710 105.930 # SOURCE3 19 1.1883 + angle_coeff @angle:cl-c3-h2 harmonic 43.490 107.140 # SOURCE4 50 0.5973 + angle_coeff @angle:cl-c3-hc harmonic 43.360 107.650 # SOURCE2 2 2.2500 + angle_coeff @angle:cl-c3-os harmonic 64.920 111.400 # SOURCE4 8 0.8275 + angle_coeff @angle:cl-c3-ss harmonic 78.390 112.940 # SOURCE4 10 1.4625 + angle_coeff @angle:c-c3-n2 harmonic 66.920 109.550 # SOURCE4 55 1.4579 + angle_coeff @angle:c-c3-n3 harmonic 66.590 111.140 # SOURCE4 629 1.6673 + angle_coeff @angle:c-c3-n4 harmonic 65.070 114.210 # SOURCE4 27 1.5388 + angle_coeff @angle:c-c3-n harmonic 66.670 111.560 # SOURCE3 28 1.7981 + angle_coeff @angle:c-c3-na harmonic 66.810 111.370 # SOURCE4 31 1.6229 + angle_coeff @angle:c-c3-nh harmonic 67.360 109.430 # SOURCE4 42 1.7022 + angle_coeff @angle:c-c3-oh harmonic 68.650 108.700 # SOURCE4 299 1.3415 + angle_coeff @angle:c-c3-os harmonic 68.030 109.820 # SOURCE3 10 2.0612 + angle_coeff @angle:c-c3-p5 harmonic 62.230 110.410 # SOURCE4 15 2.2683 + angle_coeff @angle:c-c3-s6 harmonic 80.060 110.220 # SOURCE4 5 2.0076 + angle_coeff @angle:c-c3-sh harmonic 79.050 108.820 # SOURCE4 12 0.8354 + angle_coeff @angle:c-c3-ss harmonic 78.090 111.580 # SOURCE3 5 1.9506 + angle_coeff @angle:cx-c3-cx harmonic 63.530 112.580 # SOURCE4 7 1.2211 + angle_coeff @angle:cx-c3-h1 harmonic 47.040 109.640 # SOURCE4 175 0.8822 + angle_coeff @angle:cx-c3-hc harmonic 46.920 110.200 # SOURCE4 356 0.8798 + angle_coeff @angle:cx-c3-hx harmonic 46.380 112.810 # SOURCE4 12 0.0977 + angle_coeff @angle:cx-c3-n3 harmonic 65.830 113.220 # SOURCE4 33 1.3978 + angle_coeff @angle:cx-c3-n4 harmonic 68.880 101.510 # SOURCE4 12 0.0760 + angle_coeff @angle:cx-c3-n harmonic 66.220 112.590 # SOURCE4 22 0.8034 + angle_coeff @angle:cx-c3-oh harmonic 68.100 109.970 # SOURCE4 25 1.3176 + angle_coeff @angle:cx-c3-os harmonic 68.400 108.160 # SOURCE4 26 1.0162 + angle_coeff @angle:cy-c3-h1 harmonic 47.000 107.880 # SOURCE4 162 0.9624 + angle_coeff @angle:cy-c3-hc harmonic 46.510 110.170 # SOURCE3 16 0.5693 + angle_coeff @angle:cy-c3-n3 harmonic 65.630 112.720 # SOURCE4 7 1.0639 + angle_coeff @angle:cy-c3-oh harmonic 67.220 111.560 # SOURCE4 138 0.5051 + angle_coeff @angle:cy-c3-os harmonic 68.450 106.790 # SOURCE4 5 1.0955 + angle_coeff @angle:f-c3-f harmonic 71.260 107.160 # SOURCE2 10 1.1324 + angle_coeff @angle:f-c3-h1 harmonic 51.570 107.850 # SOURCE3 14 0.9537 + angle_coeff @angle:f-c3-h2 harmonic 51.360 108.410 # SOURCE3 6 0.5081 + angle_coeff @angle:f-c3-h3 harmonic 51.050 110.010 # SOURCE4 19 0.6811 + angle_coeff @angle:f-c3-hc harmonic 51.330 108.920 # SOURCE2 5 3.0534 + angle_coeff @angle:f-c3-n2 harmonic 69.230 110.400 # SOURCE2 3 2.6470 + angle_coeff @angle:f-c3-os harmonic 70.660 110.610 # SOURCE4 45 1.1755 + angle_coeff @angle:f-c3-p5 harmonic 63.700 107.250 # SOURCE4 11 1.1735 + angle_coeff @angle:f-c3-s6 harmonic 81.220 109.670 # SOURCE4 24 0.4116 + angle_coeff @angle:f-c3-ss harmonic 78.640 111.890 # SOURCE4 11 0.9479 + angle_coeff @angle:h1-c3-h1 harmonic 39.180 109.550 # SOURCE3 1888 1.1205 + angle_coeff @angle:h1-c3-n1 harmonic 49.990 107.310 # HF/6-31G* 1 + angle_coeff @angle:h1-c3-n2 harmonic 49.260 109.610 # SOURCE3 63 1.0452 + angle_coeff @angle:h1-c3-n3 harmonic 49.390 109.920 # SOURCE3 313 1.1810 + angle_coeff @angle:h1-c3-n harmonic 49.820 109.320 # SOURCE3 91 1.0325 + angle_coeff @angle:h1-c3-na harmonic 49.900 109.450 # SOURCE3 53 0.9555 + angle_coeff @angle:h1-c3-nc harmonic 50.110 108.570 # SOURCE3 6 0.0764 + angle_coeff @angle:h1-c3-nd harmonic 50.110 108.570 # SOURCE3 6 same_as_h1-c3-nc + angle_coeff @angle:h1-c3-nh harmonic 49.730 109.960 # SOURCE3 70 0.7000 + angle_coeff @angle:h1-c3-no harmonic 48.660 105.150 # SOURCE4 16 0.4950 + angle_coeff @angle:h1-c3-o harmonic 52.530 117.190 # SOURCE3 6 0.0003 + angle_coeff @angle:h1-c3-oh harmonic 50.970 109.880 # SOURCE3 63 1.3172 + angle_coeff @angle:h1-c3-os harmonic 50.840 108.820 # SOURCE3 541 0.8042 + angle_coeff @angle:h1-c3-p5 harmonic 42.870 107.990 # SOURCE4 72 1.1862 + angle_coeff @angle:h1-c3-s4 harmonic 54.280 108.660 # SOURCE3 201 0.3834 + angle_coeff @angle:h1-c3-s harmonic 52.120 112.600 # SOURCE3 6 0.0026 + angle_coeff @angle:h1-c3-s6 harmonic 55.510 108.110 # SOURCE3 160 0.5518 + angle_coeff @angle:h1-c3-sh harmonic 53.660 109.210 # SOURCE3 22 1.2028 + angle_coeff @angle:h1-c3-ss harmonic 53.660 109.340 # SOURCE3 356 0.6573 + angle_coeff @angle:h1-c3-sx harmonic 54.210 108.690 # SOURCE3 90 0.2749 + angle_coeff @angle:h1-c3-sy harmonic 55.250 108.090 # SOURCE3 93 0.2556 + angle_coeff @angle:h2-c3-h2 harmonic 39.000 109.190 # SOURCE3 29 3.1352 + angle_coeff @angle:h2-c3-i harmonic 38.690 104.990 # SOURCE3 2 0.0000 + angle_coeff @angle:h2-c3-n2 harmonic 49.080 110.220 # SOURCE3 6 0.2133 + angle_coeff @angle:h2-c3-n3 harmonic 49.370 109.800 # SOURCE4 189 1.2893 + angle_coeff @angle:h2-c3-n harmonic 50.220 107.380 # SOURCE4 258 1.3140 + angle_coeff @angle:h2-c3-na harmonic 50.270 107.660 # SOURCE3 6 1.4096 + angle_coeff @angle:h2-c3-nc harmonic 49.850 109.470 # SOURCE3 10 0.3133 + angle_coeff @angle:h2-c3-nd harmonic 49.850 109.470 # SOURCE3 10 same_as_h2-c3-nc + angle_coeff @angle:h2-c3-nh harmonic 49.600 110.330 # SOURCE4 102 1.0596 + angle_coeff @angle:h2-c3-no harmonic 47.830 108.690 # SOURCE3 4 0.0000 + angle_coeff @angle:h2-c3-o harmonic 54.380 108.970 # SOURCE3 4 0.0000 + angle_coeff @angle:h2-c3-oh harmonic 51.290 108.300 # SOURCE3 6 0.5715 + angle_coeff @angle:h2-c3-os harmonic 50.840 108.580 # SOURCE3 44 1.2773 + angle_coeff @angle:h2-c3-s4 harmonic 54.330 108.580 # SOURCE3 8 0.2408 + angle_coeff @angle:h2-c3-s harmonic 53.560 106.750 # SOURCE3 4 0.0000 + angle_coeff @angle:h2-c3-s6 harmonic 55.940 106.540 # SOURCE4 27 0.9934 + angle_coeff @angle:h2-c3-sh harmonic 54.020 107.870 # SOURCE3 6 0.4376 + angle_coeff @angle:h2-c3-ss harmonic 53.590 109.750 # SOURCE3 10 0.3442 + angle_coeff @angle:h3-c3-n3 harmonic 49.730 108.390 # SOURCE4 12 1.7932 + angle_coeff @angle:h3-c3-nc harmonic 49.910 109.370 # SOURCE3 1 0.0000 + angle_coeff @angle:h3-c3-nd harmonic 49.910 109.370 # SOURCE3 1 same_as_h3-c3-nc + angle_coeff @angle:h3-c3-nh harmonic 49.530 110.780 # SOURCE4 5 1.5993 + angle_coeff @angle:h3-c3-os harmonic 50.090 112.030 # SOURCE4 17 1.0957 + angle_coeff @angle:h3-c3-ss harmonic 53.680 109.270 # SOURCE4 8 0.8367 + angle_coeff @angle:hc-c3-hc harmonic 39.430 108.350 # SOURCE3 2380 0.9006 + angle_coeff @angle:hc-c3-i harmonic 38.620 104.990 # SOURCE3 1 + angle_coeff @angle:hc-c3-n2 harmonic 49.290 109.500 # SOURCE3 1 + angle_coeff @angle:hc-c3-n3 harmonic 49.420 109.800 # SOURCE2 5 2.0070 + angle_coeff @angle:hc-c3-n4 harmonic 49.010 107.900 # SOURCE3 1 + angle_coeff @angle:hc-c3-n harmonic 49.780 109.500 # SOURCE3 1 + angle_coeff @angle:hc-c3-na harmonic 49.900 109.500 # SOURCE3 1 + angle_coeff @angle:hc-c3-nh harmonic 49.380 111.540 # SOURCE3 1 + angle_coeff @angle:hc-c3-no harmonic 48.190 107.200 # SOURCE2 1 0.0000 + angle_coeff @angle:hc-c3-oh harmonic 51.070 109.500 # SOURCE3 1 + angle_coeff @angle:hc-c3-os harmonic 50.870 108.700 # SOURCE2 13 2.3739 + angle_coeff @angle:hc-c3-p2 harmonic 41.380 110.180 # SOURCE3 25 0.4057 + angle_coeff @angle:hc-c3-p3 harmonic 41.660 110.140 # SOURCE3 325 0.5126 + angle_coeff @angle:hc-c3-p4 harmonic 42.040 109.590 # SOURCE3 87 0.3196 + angle_coeff @angle:hc-c3-p5 harmonic 42.540 109.640 # SOURCE3 69 0.8112 + angle_coeff @angle:hc-c3-px harmonic 42.240 109.740 # SOURCE3 84 0.3474 + angle_coeff @angle:hc-c3-py harmonic 42.560 109.540 # SOURCE3 39 0.1999 + angle_coeff @angle:hc-c3-s4 harmonic 54.570 107.500 # SOURCE2 1 0.0000 + angle_coeff @angle:hc-c3-s6 harmonic 55.480 108.200 # SOURCE3 1 + angle_coeff @angle:hc-c3-sh harmonic 53.990 107.870 # SOURCE2 3 2.0981 + angle_coeff @angle:hc-c3-ss harmonic 53.800 108.760 # SOURCE2 3 1.6891 + angle_coeff @angle:hx-c3-hx harmonic 39.040 110.740 # SOURCE3 137 0.5531 + angle_coeff @angle:hx-c3-n4 harmonic 49.020 107.910 # SOURCE3 148 0.5899 + angle_coeff @angle:i-c3-i harmonic 61.980 113.120 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-c3-n1 harmonic 71.090 105.070 # HF/6-31G* 1 + angle_coeff @angle:n2-c3-n2 harmonic 69.890 107.700 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-c3-nh harmonic 69.260 111.060 # SOURCE4 5 0.7868 + angle_coeff @angle:n2-c3-oh harmonic 70.150 111.820 # SOURCE4 10 0.3451 + angle_coeff @angle:n2-c3-os harmonic 70.040 111.230 # SOURCE4 6 1.0463 + angle_coeff @angle:n3-c3-n3 harmonic 69.610 109.590 # SOURCE4 27 1.8125 + angle_coeff @angle:n3-c3-nc harmonic 68.790 113.290 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-c3-nd harmonic 68.790 113.290 # SOURCE3 1 same_as_n3-c3-nc + angle_coeff @angle:n3-c3-nh harmonic 69.740 110.080 # SOURCE4 21 1.0686 + angle_coeff @angle:n3-c3-oh harmonic 70.710 110.630 # SOURCE4 20 1.0177 + angle_coeff @angle:n3-c3-os harmonic 71.150 108.330 # SOURCE4 17 1.9545 + angle_coeff @angle:n3-c3-p5 harmonic 64.440 109.510 # SOURCE4 10 1.5002 + angle_coeff @angle:n3-c3-ss harmonic 81.950 107.730 # SOURCE4 18 1.7621 + angle_coeff @angle:n4-c3-n4 harmonic 67.130 113.320 # SOURCE3 1 0.0000 + angle_coeff @angle:na-c3-na harmonic 69.060 113.490 # SOURCE3 1 0.0000 + angle_coeff @angle:na-c3-os harmonic 71.270 109.060 # SOURCE4 170 0.5450 + angle_coeff @angle:nc-c3-nc harmonic 69.960 110.610 # SOURCE3 1 0.0000 + angle_coeff @angle:nc-c3-nh harmonic 69.340 112.430 # SOURCE3 1 0.0000 + angle_coeff @angle:nc-c3-os harmonic 69.280 115.410 # SOURCE3 3 1.0288 + angle_coeff @angle:nd-c3-nd harmonic 69.960 110.610 # SOURCE3 1 same_as_nc-c3-nc + angle_coeff @angle:nd-c3-nh harmonic 69.340 112.430 # SOURCE3 1 same_as_nc-c3-nh + angle_coeff @angle:nd-c3-os harmonic 69.280 115.410 # SOURCE3 3 same_as_nc-c3-os + angle_coeff @angle:nh-c3-nh harmonic 71.410 105.870 # SOURCE3 1 0.0000 + angle_coeff @angle:nh-c3-oh harmonic 70.470 112.360 # SOURCE4 12 0.7775 + angle_coeff @angle:nh-c3-os harmonic 71.260 108.930 # SOURCE4 17 1.3775 + angle_coeff @angle:nh-c3-p5 harmonic 63.700 112.500 # SOURCE4 5 1.7371 + angle_coeff @angle:nh-c3-ss harmonic 81.670 108.880 # SOURCE4 8 2.1521 + angle_coeff @angle:n-c3-n2 harmonic 68.820 112.340 # SOURCE4 5 1.1443 + angle_coeff @angle:n-c3-n3 harmonic 69.390 111.030 # SOURCE4 15 1.8216 + angle_coeff @angle:n-c3-n harmonic 68.780 113.810 # SOURCE3 1 0.0000 + angle_coeff @angle:n-c3-nh harmonic 70.540 108.340 # SOURCE4 11 2.1727 + angle_coeff @angle:n-c3-oh harmonic 70.360 112.540 # SOURCE4 31 1.1295 + angle_coeff @angle:no-c3-no harmonic 68.370 104.470 # SOURCE4 5 0.9726 + angle_coeff @angle:n-c3-os harmonic 71.140 109.160 # SOURCE4 153 0.8778 + angle_coeff @angle:n-c3-p5 harmonic 64.380 110.050 # SOURCE4 5 1.2965 + angle_coeff @angle:oh-c3-oh harmonic 72.710 109.230 # SOURCE4 8 1.4978 + angle_coeff @angle:oh-c3-os harmonic 72.380 109.210 # SOURCE4 85 1.1964 + angle_coeff @angle:oh-c3-p5 harmonic 65.440 108.860 # SOURCE4 33 1.2025 + angle_coeff @angle:oh-c3-sh harmonic 80.110 115.460 # SOURCE3 1 0.0000 + angle_coeff @angle:o-c3-o harmonic 74.430 122.300 # SOURCE3 1 0.0000 + angle_coeff @angle:os-c3-os harmonic 71.720 110.240 # SOURCE3 17 2.1340 + angle_coeff @angle:os-c3-p5 harmonic 65.470 108.360 # SOURCE4 22 2.1937 + angle_coeff @angle:os-c3-ss harmonic 82.720 107.980 # SOURCE4 20 1.7464 + angle_coeff @angle:p2-c3-p2 harmonic 61.280 110.480 # SOURCE3 1 0.0000 + angle_coeff @angle:p3-c3-p3 harmonic 61.730 110.160 # SOURCE3 1 0.0000 + angle_coeff @angle:p5-c3-p5 harmonic 62.800 110.130 # SOURCE4 33 2.4116 + angle_coeff @angle:p5-c3-ss harmonic 78.880 111.300 # SOURCE4 5 2.0560 + angle_coeff @angle:s4-c3-s4 harmonic 99.950 112.290 # SOURCE3 2 1.2724 + angle_coeff @angle:s4-c3-s6 harmonic 100.300 113.520 # SOURCE3 1 + angle_coeff @angle:s6-c3-s6 harmonic 102.050 111.750 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-c3-sh harmonic 97.420 116.260 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-c3-ss harmonic 99.850 110.730 # SOURCE3 1 + angle_coeff @angle:s-c3-s harmonic 93.400 123.350 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-c3-ss harmonic 99.950 110.570 # SOURCE4 15 1.4311 + angle_coeff @angle:br-ca-br harmonic 67.310 117.600 # SOURCE3 1 + angle_coeff @angle:br-ca-ca harmonic 63.480 118.130 # SOURCE3 8 0.6041 + angle_coeff @angle:c1-ca-c1 harmonic 64.700 120.000 # SOURCE3 1 + angle_coeff @angle:c1-ca-ca harmonic 65.860 120.000 # SOURCE3 1 + angle_coeff @angle:c2-ca-c2 harmonic 62.950 120.000 # SOURCE3 1 + angle_coeff @angle:c2-ca-ca harmonic 64.690 120.600 # SOURCE3 1 + angle_coeff @angle:c3-ca-c2 harmonic 62.240 120.000 # SOURCE3 1 + angle_coeff @angle:c3-ca-c3 harmonic 62.410 116.800 # SOURCE3 1 + angle_coeff @angle:c3-ca-ca harmonic 63.840 120.630 # SOURCE3 60 0.7175 + angle_coeff @angle:c3-ca-cp harmonic 63.700 120.630 # SOURCE3 60 0.7175 + angle_coeff @angle:c3-ca-cq harmonic 63.590 120.630 # SOURCE3 60 0.7175 + angle_coeff @angle:c3-ca-na harmonic 66.590 118.780 # SOURCE4 59 1.1184 + angle_coeff @angle:c3-ca-nb harmonic 67.330 116.660 # SOURCE4 408 0.9380 + angle_coeff @angle:ca-ca-ca harmonic 67.180 119.970 # SOURCE3 1969 0.3480 + angle_coeff @angle:ca-ca-cc harmonic 65.990 120.100 # SOURCE3 103 0.3451 + angle_coeff @angle:ca-ca-cd harmonic 65.990 120.100 # SOURCE3 103 0.3451 + angle_coeff @angle:ca-ca-ce harmonic 64.880 120.660 # SOURCE3 14 0.1564 + angle_coeff @angle:ca-ca-cf harmonic 64.880 120.660 # SOURCE3 14 same_as_ca-ca-ce + angle_coeff @angle:ca-ca-cg harmonic 65.900 120.050 # SOURCE3 6 0.2397 + angle_coeff @angle:ca-ca-ch harmonic 65.900 120.050 # SOURCE3 6 same_as_ca-ca-cg + angle_coeff @angle:ca-ca-cl harmonic 62.920 119.400 # SOURCE4 2459 0.5283 + angle_coeff @angle:ca-ca-cp harmonic 67.240 119.070 # SOURCE3 14 2.3077 + angle_coeff @angle:ca-ca-cq harmonic 67.090 119.070 # SOURCE3 14 2.3077 + angle_coeff @angle:ca-ca-cx harmonic 64.480 120.830 # SOURCE4 71 1.3062 + angle_coeff @angle:ca-ca-cy harmonic 63.770 120.860 # SOURCE4 17 2.0287 + angle_coeff @angle:ca-ca-f harmonic 67.510 118.950 # SOURCE4 967 0.3369 + angle_coeff @angle:ca-ca-h4 harmonic 48.240 121.090 # SOURCE3 57 1.4696 + angle_coeff @angle:ca-ca-ha harmonic 48.460 120.010 # SOURCE3 2980 0.2511 + angle_coeff @angle:ca-ca-i harmonic 58.590 118.470 # SOURCE3 10 0.6181 + angle_coeff @angle:ca-ca-n1 harmonic 68.920 118.500 # HF/6-31G* 1 + angle_coeff @angle:ca-ca-n2 harmonic 70.950 119.570 # SOURCE3 1 + angle_coeff @angle:ca-ca-n4 harmonic 67.280 118.410 # SOURCE3 6 0.1691 + angle_coeff @angle:ca-ca-n harmonic 67.970 119.890 # SOURCE3 18 0.2095 + angle_coeff @angle:ca-ca-na harmonic 70.210 118.340 # SOURCE3 54 3.6168 + angle_coeff @angle:ca-ca-nb harmonic 69.160 122.630 # SOURCE3 83 1.1249 + angle_coeff @angle:ca-ca-nc harmonic 70.140 119.720 # SOURCE3 22 3.3994 + angle_coeff @angle:ca-ca-nd harmonic 70.140 119.720 # SOURCE3 22 3.3994 + angle_coeff @angle:ca-ca-ne harmonic 67.740 119.880 # SOURCE3 24 0.3637 + angle_coeff @angle:ca-ca-nf harmonic 67.740 119.880 # SOURCE3 24 0.3637 + angle_coeff @angle:ca-ca-nh harmonic 69.340 120.130 # SOURCE3 193 0.6341 + angle_coeff @angle:ca-ca-no harmonic 66.880 119.540 # SOURCE3 10 1.3187 + angle_coeff @angle:ca-ca-o harmonic 71.850 123.290 # SOURCE4 11 1.2526 + angle_coeff @angle:ca-ca-oh harmonic 69.850 119.940 # SOURCE3 14 0.1627 + angle_coeff @angle:ca-ca-os harmonic 69.790 119.200 # SOURCE3 52 0.5240 + angle_coeff @angle:ca-ca-p2 harmonic 61.520 114.360 # SOURCE3 1 + angle_coeff @angle:ca-ca-p3 harmonic 60.320 120.730 # SOURCE3 6 0.1273 + angle_coeff @angle:ca-ca-p4 harmonic 60.930 120.300 # SOURCE3 1 + angle_coeff @angle:ca-ca-p5 harmonic 61.240 120.280 # SOURCE4 5 0.0177 + angle_coeff @angle:ca-ca-pe harmonic 60.250 120.450 # SOURCE3 20 0.2719 + angle_coeff @angle:ca-ca-pf harmonic 60.250 120.450 # SOURCE3 20 0.2719 + angle_coeff @angle:ca-ca-px harmonic 60.340 120.530 # SOURCE3 10 0.4509 + angle_coeff @angle:ca-ca-py harmonic 61.180 119.980 # SOURCE3 6 0.0670 + angle_coeff @angle:ca-ca-s4 harmonic 78.120 119.150 # SOURCE3 1 + angle_coeff @angle:ca-ca-s6 harmonic 78.690 120.540 # SOURCE4 36 1.2154 + angle_coeff @angle:ca-ca-s harmonic 78.750 122.550 # SOURCE3 4 0.0000 + angle_coeff @angle:ca-ca-sh harmonic 77.610 121.780 # SOURCE4 17 1.2849 + angle_coeff @angle:ca-ca-ss harmonic 78.500 119.930 # SOURCE3 16 0.3901 + angle_coeff @angle:ca-ca-sx harmonic 76.800 119.180 # SOURCE3 6 0.0434 + angle_coeff @angle:ca-ca-sy harmonic 78.020 119.890 # SOURCE3 24 1.8813 + angle_coeff @angle:c-ca-c3 harmonic 62.610 118.060 # SOURCE3 1 + angle_coeff @angle:c-ca-c harmonic 62.650 120.000 # SOURCE3 1 + angle_coeff @angle:c-ca-ca harmonic 64.640 120.140 # SOURCE3 40 0.4788 + angle_coeff @angle:cc-ca-cp harmonic 64.690 124.300 # SOURCE4 10 0.6423 + angle_coeff @angle:cc-ca-nb harmonic 69.060 118.450 # SOURCE4 35 1.6594 + angle_coeff @angle:cd-ca-nb harmonic 69.340 117.500 # SOURCE4 29 1.8623 + angle_coeff @angle:ce-ca-na harmonic 67.440 119.850 # SOURCE4 9 0.7001 + angle_coeff @angle:ce-ca-nb harmonic 68.300 117.380 # SOURCE4 32 0.6890 + angle_coeff @angle:cf-ca-nb harmonic 68.080 118.140 # SOURCE4 12 1.1775 + angle_coeff @angle:cg-ca-cp harmonic 65.330 121.530 # SOURCE4 12 0.1831 + angle_coeff @angle:c-ca-ha harmonic 46.510 115.900 # SOURCE3 1 + angle_coeff @angle:cl-ca-cl harmonic 62.630 118.720 # SOURCE3 1 + angle_coeff @angle:cl-ca-cp harmonic 62.600 120.310 # SOURCE4 18 0.5607 + angle_coeff @angle:cl-ca-nb harmonic 65.810 116.150 # SOURCE4 50 0.6047 + angle_coeff @angle:c-ca-nb harmonic 67.710 117.940 # SOURCE4 91 1.0536 + angle_coeff @angle:c-ca-nc harmonic 64.400 130.800 # SOURCE3 1 + angle_coeff @angle:c-ca-nd harmonic 64.400 130.800 # SOURCE3 1 same_as_c-ca-nc + angle_coeff @angle:cp-ca-f harmonic 67.180 119.390 # SOURCE4 16 0.1724 + angle_coeff @angle:cp-ca-h4 harmonic 48.230 120.030 # SOURCE4 27 0.4431 + angle_coeff @angle:cp-ca-ha harmonic 48.030 121.080 # SOURCE3 12 1.7484 + angle_coeff @angle:cp-ca-na harmonic 73.000 108.790 # SOURCE4 165 0.5166 + angle_coeff @angle:cp-ca-nb harmonic 68.640 123.720 # SOURCE4 50 0.8176 + angle_coeff @angle:cp-ca-nh harmonic 68.740 121.520 # SOURCE4 11 0.5438 + angle_coeff @angle:cp-ca-oh harmonic 69.340 120.960 # SOURCE4 12 1.1400 + angle_coeff @angle:cp-ca-ss harmonic 80.870 112.750 # SOURCE4 8 0.6216 + angle_coeff @angle:cp-ca-sy harmonic 80.930 111.180 # SOURCE3 2 0.0000 + angle_coeff @angle:cq-ca-ha harmonic 47.860 121.080 # SOURCE3 12 1.7484 + angle_coeff @angle:cq-ca-sy harmonic 80.860 111.180 # SOURCE3 2 0.0000 + angle_coeff @angle:f-ca-f harmonic 68.050 117.500 # SOURCE3 1 + angle_coeff @angle:f-ca-nb harmonic 71.690 114.580 # SOURCE4 19 0.2987 + angle_coeff @angle:h4-ca-n harmonic 49.480 116.020 # SOURCE3 1 + angle_coeff @angle:h4-ca-na harmonic 51.880 114.650 # SOURCE3 5 1.5484 + angle_coeff @angle:h4-ca-nb harmonic 51.820 115.940 # SOURCE3 52 0.7370 + angle_coeff @angle:h4-ca-nc harmonic 51.460 118.360 # SOURCE3 1 + angle_coeff @angle:h4-ca-nd harmonic 51.460 118.360 # SOURCE3 1 same_as_h4-ca-nc + angle_coeff @angle:h4-ca-os harmonic 52.300 111.150 # SOURCE3 1 + angle_coeff @angle:h4-ca-ss harmonic 53.660 116.190 # SOURCE3 1 + angle_coeff @angle:h5-ca-nb harmonic 51.760 116.350 # SOURCE3 30 0.5545 + angle_coeff @angle:h5-ca-nc harmonic 50.700 122.110 # SOURCE3 1 + angle_coeff @angle:h5-ca-nd harmonic 50.700 122.110 # SOURCE3 1 same_as_h5-ca-nc + angle_coeff @angle:ha-ca-n2 harmonic 52.970 116.000 # SOURCE2 1 0.0000 + angle_coeff @angle:ha-ca-p2 harmonic 39.570 122.560 # SOURCE3 1 + angle_coeff @angle:i-ca-i harmonic 62.290 119.280 # SOURCE3 1 + angle_coeff @angle:n1-ca-n1 harmonic 70.730 117.030 # HF/6-31G* 1 + angle_coeff @angle:n2-ca-n2 harmonic 75.050 120.000 # SOURCE3 1 + angle_coeff @angle:n2-ca-na harmonic 73.800 119.600 # SOURCE3 1 + angle_coeff @angle:n4-ca-n4 harmonic 67.650 116.820 # SOURCE3 1 + angle_coeff @angle:na-ca-na harmonic 76.480 107.650 # SOURCE4 5 0.8751 + angle_coeff @angle:na-ca-nb harmonic 70.600 127.070 # SOURCE4 237 1.9392 + angle_coeff @angle:na-ca-nh harmonic 72.480 118.620 # SOURCE4 29 0.9759 + angle_coeff @angle:nb-ca-nb harmonic 70.780 127.190 # SOURCE4 585 1.1793 + angle_coeff @angle:nb-ca-nc harmonic 70.900 127.320 # SOURCE4 8 0.8052 + angle_coeff @angle:nb-ca-nd harmonic 71.250 126.080 # SOURCE4 14 0.9814 + angle_coeff @angle:nb-ca-nh harmonic 73.200 116.950 # SOURCE4 765 0.8040 + angle_coeff @angle:nb-ca-oh harmonic 73.570 117.300 # SOURCE4 64 0.9290 + angle_coeff @angle:nb-ca-os harmonic 72.540 119.660 # SOURCE4 76 0.6493 + angle_coeff @angle:nb-ca-sh harmonic 81.390 117.590 # SOURCE4 15 1.4616 + angle_coeff @angle:nb-ca-ss harmonic 81.120 119.300 # SOURCE4 41 1.3420 + angle_coeff @angle:nc-ca-nc harmonic 70.670 128.740 # SOURCE3 1 + angle_coeff @angle:nc-ca-nh harmonic 72.770 118.860 # SOURCE3 1 + angle_coeff @angle:nd-ca-nd harmonic 70.670 128.740 # SOURCE3 1 same_as_nc-ca-nc + angle_coeff @angle:nd-ca-nh harmonic 72.770 118.860 # SOURCE3 1 same_as_nc-ca-nh + angle_coeff @angle:nh-ca-nh harmonic 71.400 120.980 # SOURCE3 1 + angle_coeff @angle:n-ca-nc harmonic 69.660 123.860 # SOURCE3 1 + angle_coeff @angle:n-ca-nd harmonic 69.660 123.860 # SOURCE3 1 same_as_n-ca-nc + angle_coeff @angle:n-ca-nh harmonic 71.290 116.160 # SOURCE3 1 + angle_coeff @angle:no-ca-no harmonic 67.420 117.140 # SOURCE3 1 + angle_coeff @angle:oh-ca-oh harmonic 72.630 120.000 # SOURCE3 1 + angle_coeff @angle:o-ca-o harmonic 78.210 126.820 # SOURCE3 1 + angle_coeff @angle:os-ca-os harmonic 74.010 113.730 # SOURCE3 1 + angle_coeff @angle:p2-ca-p2 harmonic 58.980 121.200 # SOURCE3 1 + angle_coeff @angle:p3-ca-p3 harmonic 59.440 121.460 # SOURCE3 1 + angle_coeff @angle:p5-ca-p5 harmonic 60.760 120.000 # SOURCE3 1 + angle_coeff @angle:s4-ca-s4 harmonic 104.060 105.810 # SOURCE3 1 + angle_coeff @angle:s6-ca-s6 harmonic 105.770 105.810 # SOURCE3 1 + angle_coeff @angle:sh-ca-sh harmonic 98.150 120.240 # SOURCE3 1 + angle_coeff @angle:s-ca-s harmonic 98.380 125.140 # SOURCE3 1 + angle_coeff @angle:ss-ca-ss harmonic 100.760 115.150 # SOURCE3 1 + angle_coeff @angle:br-c-br harmonic 66.910 113.100 # SOURCE3 1 + angle_coeff @angle:br-c-c3 harmonic 63.340 110.740 # SOURCE3 1 0.0000 + angle_coeff @angle:br-c-o harmonic 63.190 121.460 # SOURCE3 5 1.6264 + angle_coeff @angle:c1-c-c1 harmonic 65.090 115.320 # SOURCE3 1 + angle_coeff @angle:c1-c-o harmonic 69.920 122.340 # SOURCE3 1 + angle_coeff @angle:c2-c-c2 harmonic 67.170 116.780 # SOURCE3 1 + angle_coeff @angle:c2-c-ha harmonic 48.650 115.950 # SOURCE3 1 + angle_coeff @angle:c2-c-o harmonic 72.770 119.120 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-c-s harmonic 81.850 119.160 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-c-c3 harmonic 62.820 116.050 # SOURCE3 11 1.0986 + angle_coeff @angle:c3-c-ca harmonic 62.590 118.540 # SOURCE4 240 1.3614 + angle_coeff @angle:c3-c-cc harmonic 63.240 118.000 # SOURCE4 21 0.9834 + angle_coeff @angle:c3-c-cd harmonic 63.500 117.020 # SOURCE4 25 1.4755 + angle_coeff @angle:c3-c-ce harmonic 63.470 116.250 # SOURCE4 188 1.1613 + angle_coeff @angle:c3-c-cf harmonic 63.300 116.860 # SOURCE4 45 1.5859 + angle_coeff @angle:c3-c-cg harmonic 64.260 115.000 # SOURCE2 1 0.0000 + angle_coeff @angle:c3-c-ch harmonic 64.260 115.000 # SOURCE2 1 same_as_c3-c-cg + angle_coeff @angle:c3-c-cl harmonic 62.560 111.990 # SOURCE3 2 0.0125 + angle_coeff @angle:c3-c-f harmonic 66.930 110.700 # SOURCE2 1 0.0000 + angle_coeff @angle:c3-c-h4 harmonic 46.110 114.400 # SOURCE4 57 0.4032 + angle_coeff @angle:c3-c-ha harmonic 46.010 115.220 # SOURCE3 15 0.3181 + angle_coeff @angle:c3-c-i harmonic 56.870 112.940 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-c-n2 harmonic 66.620 114.530 # SOURCE3 1 + angle_coeff @angle:c3-c-n4 harmonic 64.610 112.260 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-c-n harmonic 67.860 115.150 # SOURCE3 153 2.7443 + angle_coeff @angle:c3-c-ne harmonic 68.090 111.390 # SOURCE4 11 2.1430 + angle_coeff @angle:c3-c-nf harmonic 67.430 113.380 # SOURCE3 1 same_as_c3-c-ne + angle_coeff @angle:c3-c-o harmonic 68.030 123.110 # SOURCE3 267 3.0977 + angle_coeff @angle:c3-c-oh harmonic 69.840 112.200 # SOURCE3 14 1.8324 + angle_coeff @angle:c3-c-os harmonic 69.260 111.960 # SOURCE3 15 2.3072 + angle_coeff @angle:c3-c-p3 harmonic 58.900 116.420 # SOURCE3 3 0.1291 + angle_coeff @angle:c3-c-p5 harmonic 58.320 118.900 # SOURCE3 1 + angle_coeff @angle:c3-c-pe harmonic 58.620 114.850 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-c-pf harmonic 58.620 114.850 # SOURCE3 1 same_as_c3-c-pe + angle_coeff @angle:c3-c-px harmonic 58.600 115.600 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-c-py harmonic 58.850 118.160 # SOURCE3 3 1.0735 + angle_coeff @angle:c3-c-s4 harmonic 75.480 114.790 # SOURCE3 1 + angle_coeff @angle:c3-c-s6 harmonic 75.500 114.720 # SOURCE3 1 + angle_coeff @angle:c3-c-s harmonic 78.510 123.730 # SOURCE3 9 1.4528 + angle_coeff @angle:c3-c-sh harmonic 78.430 114.210 # SOURCE3 3 2.3916 + angle_coeff @angle:c3-c-ss harmonic 78.990 114.320 # SOURCE3 5 2.7478 + angle_coeff @angle:c3-c-sx harmonic 75.280 113.970 # SOURCE3 3 0.0610 + angle_coeff @angle:c3-c-sy harmonic 75.800 114.280 # SOURCE3 3 0.7341 + angle_coeff @angle:ca-c-ca harmonic 63.030 118.580 # SOURCE4 144 2.1146 + angle_coeff @angle:ca-c-cc harmonic 64.370 115.570 # SOURCE4 175 1.7981 + angle_coeff @angle:ca-c-cd harmonic 63.940 117.130 # SOURCE4 82 1.7238 + angle_coeff @angle:ca-c-ce harmonic 63.290 118.610 # SOURCE4 30 1.3375 + angle_coeff @angle:ca-c-cf harmonic 62.800 120.470 # SOURCE4 6 1.3008 + angle_coeff @angle:ca-c-h4 harmonic 46.520 115.140 # SOURCE4 30 0.7320 + angle_coeff @angle:ca-c-ha harmonic 46.800 114.120 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-c-n harmonic 68.470 115.140 # SOURCE4 571 1.4648 + angle_coeff @angle:ca-c-ne harmonic 67.750 114.390 # SOURCE4 5 0.2958 + angle_coeff @angle:ca-c-o harmonic 68.670 123.440 # SOURCE3 18 2.5574 + angle_coeff @angle:ca-c-oh harmonic 70.110 113.440 # SOURCE4 222 0.8421 + angle_coeff @angle:ca-c-os harmonic 68.780 115.540 # SOURCE3 5 2.6708 + angle_coeff @angle:ca-c-s harmonic 79.130 123.040 # SOURCE4 12 0.7935 + angle_coeff @angle:ca-c-sh harmonic 77.270 118.630 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-c-ss harmonic 79.040 115.130 # SOURCE4 12 1.0069 + angle_coeff @angle:br-cc-c harmonic 63.980 115.680 # SOURCE4 8 0.4970 + angle_coeff @angle:br-cc-cc harmonic 61.820 124.890 # SOURCE4 8 1.9479 + angle_coeff @angle:br-cc-cd harmonic 62.260 124.560 # SOURCE4 32 2.4696 + angle_coeff @angle:br-cc-na harmonic 64.600 121.420 # SOURCE4 6 0.5507 + angle_coeff @angle:c2-cc-c3 harmonic 63.270 126.110 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-cc-ca harmonic 65.400 124.420 # SOURCE4 15 1.7107 + angle_coeff @angle:c2-cc-cc harmonic 66.340 121.390 # SOURCE4 29 2.2566 + angle_coeff @angle:c2-cc-cd harmonic 69.090 117.020 # SOURCE3 2 0.0703 + angle_coeff @angle:c2-cc-ha harmonic 48.690 122.720 # SOURCE3 2 0.0092 + angle_coeff @angle:c2-cc-n harmonic 67.740 126.900 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-cc-os harmonic 70.020 121.060 # SOURCE4 11 0.8179 + angle_coeff @angle:c-c-c3 harmonic 61.720 116.860 # SOURCE3 5 0.1653 + angle_coeff @angle:c3-cc-ca harmonic 61.830 126.430 # SOURCE4 119 1.7751 + angle_coeff @angle:c3-cc-cc harmonic 64.660 115.970 # SOURCE3 4 3.0507 + angle_coeff @angle:c3-cc-cd harmonic 64.810 119.450 # SOURCE3 35 8.2040 + angle_coeff @angle:c3-cc-cf harmonic 65.450 117.840 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-cc-ha harmonic 45.110 121.520 # SOURCE3 32 3.2091 + angle_coeff @angle:c3-cc-n2 harmonic 65.940 126.280 # SOURCE4 8 2.1234 + angle_coeff @angle:c3-cc-n harmonic 66.540 118.360 # SOURCE4 53 2.1705 + angle_coeff @angle:c3-cc-na harmonic 65.440 122.990 # SOURCE4 477 1.5214 + angle_coeff @angle:c3-cc-nc harmonic 65.880 121.000 # SOURCE4 66 0.8247 + angle_coeff @angle:c3-cc-nd harmonic 65.890 123.750 # SOURCE4 275 1.8941 + angle_coeff @angle:c3-cc-os harmonic 67.480 117.090 # SOURCE4 127 0.9464 + angle_coeff @angle:c3-cc-ss harmonic 77.460 121.680 # SOURCE4 145 0.8647 + angle_coeff @angle:c-c-c harmonic 62.300 111.680 # SOURCE3 2 6.1226 + angle_coeff @angle:c-c-ca harmonic 61.730 118.340 # SOURCE4 26 1.0692 + angle_coeff @angle:ca-cc-cc harmonic 67.660 111.040 # SOURCE3 9 7.9455 + angle_coeff @angle:ca-cc-cd harmonic 68.230 113.510 # SOURCE3 26 7.4229 + angle_coeff @angle:ca-cc-ce harmonic 62.580 127.870 # SOURCE4 11 1.7579 + angle_coeff @angle:ca-cc-h4 harmonic 45.570 128.660 # SOURCE3 10 3.1167 + angle_coeff @angle:ca-cc-ha harmonic 46.400 124.040 # SOURCE3 34 3.6691 + angle_coeff @angle:ca-cc-n harmonic 68.240 118.420 # SOURCE4 17 2.2100 + angle_coeff @angle:ca-cc-nc harmonic 67.790 120.310 # SOURCE4 46 0.6711 + angle_coeff @angle:ca-cc-nd harmonic 67.840 123.280 # SOURCE4 182 2.3863 + angle_coeff @angle:ca-cc-nh harmonic 67.460 122.450 # SOURCE4 9 1.4092 + angle_coeff @angle:ca-cc-oh harmonic 70.020 116.510 # SOURCE4 12 1.7855 + angle_coeff @angle:ca-cc-os harmonic 69.540 116.090 # SOURCE4 58 2.0472 + angle_coeff @angle:ca-cc-ss harmonic 78.690 120.980 # SOURCE4 28 1.8865 + angle_coeff @angle:c-cc-c2 harmonic 65.620 120.880 # SOURCE4 21 1.5157 + angle_coeff @angle:c-cc-c3 harmonic 64.900 112.750 # SOURCE3 4 0.2063 + angle_coeff @angle:c-cc-c harmonic 63.420 121.160 # SOURCE4 48 0.7193 + angle_coeff @angle:c-c-cc harmonic 64.020 111.670 # SOURCE3 4 5.5146 + angle_coeff @angle:c-cc-ca harmonic 63.550 122.950 # SOURCE3 1 0.0000 + angle_coeff @angle:c-cc-cc harmonic 63.720 122.690 # SOURCE3 2 0.0000 + angle_coeff @angle:cc-c-cc harmonic 64.820 115.970 # SOURCE4 37 1.4486 + angle_coeff @angle:cc-cc-cc harmonic 67.880 110.700 # SOURCE3 54 3.4091 + angle_coeff @angle:cc-cc-cd harmonic 68.160 114.190 # SOURCE3 517 6.5960 + angle_coeff @angle:cc-cc-ce harmonic 63.140 126.050 # SOURCE4 10 2.3332 + angle_coeff @angle:cc-cc-cf harmonic 65.650 123.920 # SOURCE3 1 0.0000 + angle_coeff @angle:cc-cc-cg harmonic 64.740 121.850 # SOURCE4 6 0.8146 + angle_coeff @angle:c-cc-cd harmonic 65.230 121.510 # SOURCE4 919 2.2603 + angle_coeff @angle:cc-c-cd harmonic 65.730 112.790 # SOURCE3 1 0.0000 + angle_coeff @angle:c-cc-ce harmonic 63.360 122.370 # SOURCE4 5 0.0254 + angle_coeff @angle:cc-c-ce harmonic 64.640 115.680 # SOURCE4 6 1.2033 + angle_coeff @angle:cc-cc-f harmonic 66.350 119.410 # SOURCE4 7 0.4917 + angle_coeff @angle:c-cc-cg harmonic 64.980 118.140 # SOURCE4 7 0.7745 + angle_coeff @angle:cc-cc-h4 harmonic 45.560 129.470 # SOURCE3 171 2.2734 + angle_coeff @angle:cc-cc-ha harmonic 47.460 119.260 # SOURCE4 506 1.6808 + angle_coeff @angle:c-cc-cl harmonic 62.790 116.010 # SOURCE4 19 0.9295 + angle_coeff @angle:cc-cc-n2 harmonic 69.460 121.150 # SOURCE3 6 0.4642 + angle_coeff @angle:cc-cc-n harmonic 67.950 119.890 # SOURCE3 36 0.2095 + angle_coeff @angle:cc-cc-na harmonic 72.210 106.800 # SOURCE3 33 0.6297 + angle_coeff @angle:cc-cc-nc harmonic 69.950 113.420 # SOURCE3 4 1.3957 + angle_coeff @angle:cc-cc-nd harmonic 71.150 112.560 # SOURCE3 141 4.2871 + angle_coeff @angle:cc-cc-nh harmonic 68.510 119.190 # SOURCE4 142 2.2114 + angle_coeff @angle:cc-cc-oh harmonic 69.230 119.670 # SOURCE4 10 2.3619 + angle_coeff @angle:cc-cc-os harmonic 69.380 117.090 # SOURCE4 99 2.4776 + angle_coeff @angle:cc-cc-pd harmonic 63.840 115.360 # SOURCE3 84 same_as_cd-cd-pc + angle_coeff @angle:cc-cc-ss harmonic 80.780 115.020 # SOURCE3 2 0.0000 + angle_coeff @angle:cc-cc-sy harmonic 74.830 128.360 # SOURCE4 8 0.9813 + angle_coeff @angle:c-c-cd harmonic 64.020 111.670 # SOURCE3 4 5.5146 + angle_coeff @angle:cd-cc-cd harmonic 67.630 121.160 # SOURCE4 42 2.0764 + angle_coeff @angle:cd-cc-ce harmonic 63.480 129.500 # SOURCE4 139 2.1675 + angle_coeff @angle:cd-cc-cl harmonic 61.780 123.720 # SOURCE4 48 1.9010 + angle_coeff @angle:cd-cc-f harmonic 67.420 121.080 # SOURCE4 28 0.8788 + angle_coeff @angle:cd-cc-h4 harmonic 47.190 129.110 # SOURCE3 418 3.1355 + angle_coeff @angle:cd-cc-ha harmonic 48.350 122.890 # SOURCE3 584 2.9334 + angle_coeff @angle:cd-cc-n harmonic 70.720 115.520 # SOURCE3 52 1.3322 + angle_coeff @angle:cd-cc-na harmonic 72.910 109.420 # SOURCE3 265 2.6051 + angle_coeff @angle:cd-cc-nc harmonic 70.990 114.980 # SOURCE3 23 5.3935 + angle_coeff @angle:cd-cc-nh harmonic 68.380 125.040 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-cc-no harmonic 65.780 128.950 # SOURCE4 117 1.4740 + angle_coeff @angle:cd-cc-oh harmonic 69.580 124.030 # SOURCE4 59 1.2544 + angle_coeff @angle:cd-cc-os harmonic 69.960 120.300 # SOURCE3 64 5.4354 + angle_coeff @angle:cd-cc-ss harmonic 82.940 111.220 # SOURCE4 692 1.2683 + angle_coeff @angle:cd-cc-sy harmonic 76.410 125.160 # SOURCE4 19 1.1014 + angle_coeff @angle:ce-cc-na harmonic 66.420 124.140 # SOURCE4 40 1.5665 + angle_coeff @angle:ce-cc-nc harmonic 66.980 121.700 # SOURCE4 8 1.6500 + angle_coeff @angle:ce-cc-nd harmonic 67.220 123.910 # SOURCE4 11 1.1451 + angle_coeff @angle:ce-cc-os harmonic 68.210 119.170 # SOURCE4 59 0.7385 + angle_coeff @angle:ce-cc-ss harmonic 78.460 120.940 # SOURCE4 31 1.2422 + angle_coeff @angle:c-cc-f harmonic 66.160 116.870 # SOURCE4 16 0.5322 + angle_coeff @angle:cg-cc-na harmonic 67.510 122.350 # SOURCE4 5 0.8112 + angle_coeff @angle:cg-cc-ss harmonic 78.880 120.700 # SOURCE4 12 0.9090 + angle_coeff @angle:cc-c-h4 harmonic 47.130 115.450 # SOURCE4 5 0.8021 + angle_coeff @angle:c-cc-ha harmonic 46.990 117.020 # SOURCE3 56 1.9713 + angle_coeff @angle:cl-cc-na harmonic 63.840 121.610 # SOURCE4 12 0.3436 + angle_coeff @angle:cl-cc-nd harmonic 63.930 122.510 # SOURCE4 5 1.6568 + angle_coeff @angle:cl-cc-ss harmonic 79.050 119.850 # SOURCE4 11 1.0626 + angle_coeff @angle:c-cc-n2 harmonic 68.530 120.890 # SOURCE3 1 0.0000 + angle_coeff @angle:c-cc-n harmonic 68.110 116.330 # SOURCE4 20 1.9278 + angle_coeff @angle:cc-c-n harmonic 70.190 111.860 # SOURCE3 36 2.3407 + angle_coeff @angle:c-cc-nc harmonic 66.280 123.150 # SOURCE4 23 2.1612 + angle_coeff @angle:cc-c-nd harmonic 67.520 116.400 # SOURCE4 23 1.1407 + angle_coeff @angle:c-cc-nd harmonic 70.070 112.910 # SOURCE3 1 0.0000 + angle_coeff @angle:c-cc-ne harmonic 67.110 119.880 # SOURCE4 6 0.3139 + angle_coeff @angle:cc-c-o harmonic 68.910 125.710 # SOURCE3 66 2.4784 + angle_coeff @angle:c-cc-oh harmonic 70.150 113.450 # SOURCE4 35 1.3440 + angle_coeff @angle:cc-c-oh harmonic 71.160 112.580 # SOURCE4 50 0.7342 + angle_coeff @angle:c-cc-os harmonic 67.710 119.810 # SOURCE4 52 1.7157 + angle_coeff @angle:cc-c-os harmonic 70.500 112.300 # SOURCE3 6 2.7842 + angle_coeff @angle:cc-c-s harmonic 78.050 127.940 # SOURCE4 12 0.9342 + angle_coeff @angle:cc-c-ss harmonic 80.330 112.520 # SOURCE4 10 0.6933 + angle_coeff @angle:cx-cc-nd harmonic 65.680 127.750 # SOURCE4 12 1.7156 + angle_coeff @angle:cx-cc-os harmonic 68.010 118.080 # SOURCE4 10 0.0955 + angle_coeff @angle:cd-c-cd harmonic 64.770 116.170 # SOURCE4 19 1.1663 + angle_coeff @angle:cd-c-cx harmonic 63.880 117.460 # SOURCE4 13 0.1625 + angle_coeff @angle:cd-c-n harmonic 70.190 111.860 # SOURCE3 36 2.3407 + angle_coeff @angle:cd-c-nc harmonic 68.310 115.760 # SOURCE4 10 0.7131 + angle_coeff @angle:cd-c-nd harmonic 68.300 113.750 # SOURCE4 14 0.0860 + angle_coeff @angle:cd-c-o harmonic 68.910 125.710 # SOURCE3 66 2.4784 + angle_coeff @angle:cd-c-oh harmonic 70.770 113.840 # SOURCE4 35 1.1033 + angle_coeff @angle:cd-c-os harmonic 70.500 112.300 # SOURCE3 6 2.7842 + angle_coeff @angle:ce-c-ce harmonic 64.340 115.790 # SOURCE4 73 0.4467 + angle_coeff @angle:ce-c-cf harmonic 64.040 116.890 # SOURCE4 11 1.6021 + angle_coeff @angle:ce-c-cx harmonic 63.950 116.250 # SOURCE4 6 0.6351 + angle_coeff @angle:ce-c-h4 harmonic 46.930 114.880 # SOURCE4 19 0.3355 + angle_coeff @angle:ce-c-ha harmonic 46.930 115.220 # SOURCE3 7 2.4188 + angle_coeff @angle:ce-c-n harmonic 68.880 115.010 # SOURCE3 2 0.5478 + angle_coeff @angle:ce-c-o harmonic 69.270 122.920 # SOURCE3 17 3.5085 + angle_coeff @angle:ce-c-oh harmonic 70.250 114.300 # SOURCE4 94 1.5074 + angle_coeff @angle:ce-c-os harmonic 70.050 112.620 # SOURCE4 125 2.0061 + angle_coeff @angle:ce-c-s harmonic 81.120 117.800 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-c-ss harmonic 80.920 110.390 # SOURCE4 5 0.6050 + angle_coeff @angle:cf-c-cf harmonic 64.070 116.780 # SOURCE3 1 same_as_ce-c-ce + angle_coeff @angle:cf-c-ha harmonic 46.930 115.220 # SOURCE3 7 same_as_ce-c-ha + angle_coeff @angle:cf-c-n harmonic 68.800 115.290 # SOURCE4 30 1.1758 + angle_coeff @angle:cf-c-o harmonic 69.270 122.920 # SOURCE3 17 3.5085 + angle_coeff @angle:cf-c-oh harmonic 70.490 113.530 # SOURCE4 34 2.1382 + angle_coeff @angle:cf-c-os harmonic 70.720 110.510 # SOURCE4 24 0.9128 + angle_coeff @angle:cf-c-s harmonic 81.120 117.800 # SOURCE3 1 same_as_ce-c-s + angle_coeff @angle:cg-c-cg harmonic 65.440 115.380 # SOURCE3 1 0.0000 + angle_coeff @angle:cg-c-ha harmonic 47.800 113.900 # SOURCE2 1 0.0000 + angle_coeff @angle:cg-c-o harmonic 70.210 122.310 # SOURCE3 2 0.0000 + angle_coeff @angle:c-c-h4 harmonic 44.620 116.360 # SOURCE4 5 0.5586 + angle_coeff @angle:h4-cc-n harmonic 50.390 117.620 # SOURCE3 53 0.9721 + angle_coeff @angle:h4-cc-na harmonic 50.220 119.660 # SOURCE3 294 2.4702 + angle_coeff @angle:h4-cc-nc harmonic 50.000 120.030 # SOURCE3 16 2.3863 + angle_coeff @angle:h4-cc-nd harmonic 51.390 119.110 # SOURCE3 135 1.6946 + angle_coeff @angle:h4-cc-os harmonic 52.270 111.890 # SOURCE3 61 2.3500 + angle_coeff @angle:h4-cc-ss harmonic 54.360 117.750 # SOURCE3 40 3.1156 + angle_coeff @angle:h5-cc-n harmonic 50.870 115.610 # SOURCE4 10 0.8505 + angle_coeff @angle:h5-cc-na harmonic 49.760 122.100 # SOURCE3 16 1.4626 + angle_coeff @angle:h5-cc-nc harmonic 49.290 123.700 # SOURCE3 6 0.3547 + angle_coeff @angle:h5-cc-nd harmonic 50.130 125.380 # SOURCE3 40 2.2157 + angle_coeff @angle:h5-cc-os harmonic 51.300 116.330 # SOURCE3 12 3.2919 + angle_coeff @angle:h5-cc-ss harmonic 53.390 122.000 # SOURCE3 6 0.7237 + angle_coeff @angle:c-c-ha harmonic 44.850 115.430 # SOURCE2 3 0.6549 + angle_coeff @angle:ha-cc-na harmonic 49.820 121.500 # SOURCE2 1 0.0000 + angle_coeff @angle:ha-cc-nc harmonic 50.730 116.540 # SOURCE3 5 1.4482 + angle_coeff @angle:ha-cc-nd harmonic 51.410 118.880 # SOURCE3 20 2.8923 + angle_coeff @angle:ha-cc-os harmonic 52.490 110.860 # SOURCE3 7 1.3846 + angle_coeff @angle:ha-cc-pd harmonic 42.350 121.760 # SOURCE3 84 same_as_ha-cd-pc + angle_coeff @angle:ha-cc-ss harmonic 53.490 121.640 # SOURCE2 5 1.3276 + angle_coeff @angle:ch-c-ch harmonic 65.440 115.380 # SOURCE3 1 same_as_cg-c-cg + angle_coeff @angle:ch-c-ha harmonic 47.800 113.900 # SOURCE2 1 same_as_cg-c-ha + angle_coeff @angle:ch-c-o harmonic 70.210 122.310 # SOURCE3 2 same_as_cg-c-o + angle_coeff @angle:cl-c-cl harmonic 63.330 111.300 # SOURCE2 1 0.0000 + angle_coeff @angle:cl-c-f harmonic 63.490 112.000 # SOURCE2 1 0.0000 + angle_coeff @angle:cl-c-ha harmonic 43.460 109.900 # SOURCE2 1 0.0000 + angle_coeff @angle:cl-c-o harmonic 64.280 121.510 # SOURCE3 6 1.6987 + angle_coeff @angle:cl-c-s harmonic 77.210 127.600 # SOURCE2 1 0.0000 + angle_coeff @angle:c-c-n harmonic 67.530 112.140 # SOURCE4 53 2.1247 + angle_coeff @angle:na-cc-nc harmonic 70.660 121.830 # SOURCE4 169 1.0340 + angle_coeff @angle:na-cc-nd harmonic 74.780 112.020 # SOURCE3 17 2.2434 + angle_coeff @angle:na-cc-no harmonic 68.480 124.900 # SOURCE4 48 0.7933 + angle_coeff @angle:na-cc-oh harmonic 73.310 117.260 # SOURCE4 16 0.9090 + angle_coeff @angle:na-cc-sx harmonic 80.050 117.040 # SOURCE4 13 0.4187 + angle_coeff @angle:na-cc-sy harmonic 79.760 120.550 # SOURCE4 7 1.7547 + angle_coeff @angle:n-cc-c harmonic 68.190 116.060 # SOURCE3 1 0.0000 + angle_coeff @angle:nc-cc-nd harmonic 72.510 118.690 # SOURCE3 9 6.6642 + angle_coeff @angle:nc-cc-nh harmonic 72.700 115.660 # SOURCE4 12 1.0083 + angle_coeff @angle:nc-cc-no harmonic 69.310 121.540 # SOURCE4 7 0.9221 + angle_coeff @angle:nc-cc-ss harmonic 81.790 119.860 # SOURCE3 2 0.0000 + angle_coeff @angle:nd-cc-nd harmonic 70.880 128.170 # SOURCE4 7 0.0269 + angle_coeff @angle:nd-cc-ne harmonic 69.290 129.660 # SOURCE4 7 0.4306 + angle_coeff @angle:nd-cc-nh harmonic 72.410 120.110 # SOURCE3 5 0.9313 + angle_coeff @angle:nd-cc-no harmonic 69.900 122.680 # SOURCE4 16 0.3393 + angle_coeff @angle:nd-cc-oh harmonic 72.800 122.190 # SOURCE4 11 0.7091 + angle_coeff @angle:nd-cc-os harmonic 74.240 115.060 # SOURCE4 109 2.3512 + angle_coeff @angle:nd-cc-sh harmonic 79.410 124.920 # SOURCE4 5 0.9563 + angle_coeff @angle:nd-cc-ss harmonic 84.180 114.510 # SOURCE3 8 0.3449 + angle_coeff @angle:nd-cc-sx harmonic 76.960 127.600 # SOURCE4 14 1.1650 + angle_coeff @angle:nd-cc-sy harmonic 79.280 123.080 # SOURCE4 13 1.0531 + angle_coeff @angle:ne-cc-ss harmonic 82.750 116.990 # SOURCE4 7 0.1657 + angle_coeff @angle:nh-cc-nh harmonic 72.930 115.960 # SOURCE3 1 0.0000 + angle_coeff @angle:nh-cc-os harmonic 72.780 117.270 # SOURCE4 13 0.7995 + angle_coeff @angle:nh-cc-ss harmonic 81.210 122.040 # SOURCE4 80 1.2781 + angle_coeff @angle:n-cc-n2 harmonic 74.770 114.480 # SOURCE4 15 2.3208 + angle_coeff @angle:n-cc-na harmonic 70.450 122.180 # SOURCE4 46 2.2856 + angle_coeff @angle:n-cc-nc harmonic 70.960 120.010 # SOURCE4 10 1.5583 + angle_coeff @angle:n-cc-nd harmonic 71.200 122.710 # SOURCE4 141 1.6659 + angle_coeff @angle:n-cc-nh harmonic 72.220 116.850 # SOURCE4 32 0.7619 + angle_coeff @angle:no-cc-os harmonic 71.010 117.590 # SOURCE4 62 0.2199 + angle_coeff @angle:no-cc-ss harmonic 80.690 121.100 # SOURCE4 10 0.0957 + angle_coeff @angle:n-cc-ss harmonic 80.680 123.050 # SOURCE4 38 1.0101 + angle_coeff @angle:c-c-o harmonic 67.160 120.990 # SOURCE4 233 2.0333 + angle_coeff @angle:c-c-oh harmonic 68.200 113.230 # SOURCE3 5 0.5615 + angle_coeff @angle:c-c-os harmonic 68.180 111.390 # SOURCE4 14 0.4038 + angle_coeff @angle:os-cc-ss harmonic 78.460 132.010 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-cc-ss harmonic 100.050 121.280 # SOURCE4 20 2.4461 + angle_coeff @angle:ss-cc-sy harmonic 98.380 121.770 # SOURCE4 20 0.4970 + angle_coeff @angle:cx-c-cx harmonic 85.450 64.600 # SOURCE2 1 0.0000 + angle_coeff @angle:cx-c-n harmonic 68.690 114.490 # SOURCE4 23 1.4914 + angle_coeff @angle:cx-c-o harmonic 68.880 122.820 # SOURCE4 97 2.2075 + angle_coeff @angle:cx-c-oh harmonic 70.490 112.320 # SOURCE4 10 0.6413 + angle_coeff @angle:cx-c-os harmonic 70.060 111.480 # SOURCE4 16 1.3998 + angle_coeff @angle:cy-c-cy harmonic 70.140 90.550 # SOURCE2 2 2.4500 + angle_coeff @angle:cy-c-n harmonic 75.430 91.540 # SOURCE4 249 0.5104 + angle_coeff @angle:cy-c-o harmonic 64.270 135.040 # SOURCE4 253 1.3450 + angle_coeff @angle:cy-c-oh harmonic 69.090 112.480 # SOURCE4 5 1.0793 + angle_coeff @angle:cy-c-os harmonic 74.550 94.890 # SOURCE4 8 0.6016 + angle_coeff @angle:c2-cd-c3 harmonic 63.270 126.110 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-cd-ca harmonic 64.430 128.220 # SOURCE3 1 same_as_c2-cc-ca + angle_coeff @angle:c2-cd-cc harmonic 69.090 117.020 # SOURCE3 2 same_as_c2-cc-cd + angle_coeff @angle:c2-cd-cd harmonic 65.270 125.410 # SOURCE3 3 2.0867 + angle_coeff @angle:c2-cd-ha harmonic 48.690 122.720 # SOURCE3 2 same_as_c2-cc-ha + angle_coeff @angle:c2-cd-n harmonic 67.740 126.900 # SOURCE3 1 same_as_c2-cc-n + angle_coeff @angle:c2-cd-os harmonic 70.530 119.310 # SOURCE3 2 same_as_c2-cc-os + angle_coeff @angle:c3-cd-ca harmonic 64.050 117.810 # SOURCE3 8 same_as_c3-cc-ca + angle_coeff @angle:c3-cd-cc harmonic 64.810 119.450 # SOURCE3 35 8.2040 + angle_coeff @angle:c3-cd-cd harmonic 64.660 115.970 # SOURCE3 4 3.0507 + angle_coeff @angle:c3-cd-ce harmonic 65.260 117.840 # SOURCE3 1 same_as_c3-cc-cf + angle_coeff @angle:c3-cd-ha harmonic 45.110 121.520 # SOURCE3 32 3.2091 + angle_coeff @angle:c3-cd-n2 harmonic 64.650 131.550 # SOURCE3 1 same_as_c3-cc-n2 + angle_coeff @angle:c3-cd-n harmonic 65.600 121.760 # SOURCE4 15 1.7884 + angle_coeff @angle:c3-cd-na harmonic 65.670 122.140 # SOURCE4 155 1.5600 + angle_coeff @angle:c3-cd-nc harmonic 66.940 119.910 # SOURCE4 200 1.6430 + angle_coeff @angle:c3-cd-nd harmonic 65.900 120.920 # SOURCE4 243 0.8832 + angle_coeff @angle:c3-cd-os harmonic 67.630 116.540 # SOURCE4 76 0.6353 + angle_coeff @angle:c3-cd-ss harmonic 77.510 121.530 # SOURCE4 26 1.4478 + angle_coeff @angle:ca-cd-cc harmonic 68.230 113.510 # SOURCE3 26 7.4229 + angle_coeff @angle:ca-cd-cd harmonic 67.660 111.040 # SOURCE3 9 7.9455 + angle_coeff @angle:ca-cd-ce harmonic 65.000 125.100 # SOURCE4 9 1.9265 + angle_coeff @angle:ca-cd-h4 harmonic 45.570 128.660 # SOURCE3 10 3.1167 + angle_coeff @angle:ca-cd-ha harmonic 46.400 124.040 # SOURCE3 34 3.6691 + angle_coeff @angle:ca-cd-n harmonic 72.510 104.870 # SOURCE3 1 same_as_ca-cc-n + angle_coeff @angle:ca-cd-na harmonic 67.030 123.450 # SOURCE4 39 1.9138 + angle_coeff @angle:ca-cd-nc harmonic 70.230 115.050 # SOURCE3 6 4.3938 + angle_coeff @angle:ca-cd-nd harmonic 67.650 120.810 # SOURCE4 116 1.2165 + angle_coeff @angle:ca-cd-oh harmonic 69.080 119.320 # SOURCE4 9 1.2731 + angle_coeff @angle:ca-cd-os harmonic 70.040 114.450 # SOURCE4 76 2.2248 + angle_coeff @angle:ca-cd-ss harmonic 79.130 119.640 # SOURCE4 15 1.8842 + angle_coeff @angle:c-cd-c2 harmonic 65.380 121.760 # SOURCE3 1 same_as_c-cc-c2 + angle_coeff @angle:c-cd-c3 harmonic 63.560 117.570 # SOURCE4 122 1.4868 + angle_coeff @angle:c-cd-c harmonic 63.410 121.180 # SOURCE4 16 1.9017 + angle_coeff @angle:c-cd-ca harmonic 63.550 122.950 # SOURCE3 1 same_as_c-cc-ca + angle_coeff @angle:c-cd-cc harmonic 65.280 121.320 # SOURCE4 789 2.4126 + angle_coeff @angle:cc-cd-cc harmonic 68.010 119.800 # SOURCE4 91 1.1370 + angle_coeff @angle:cc-cd-cd harmonic 68.160 114.190 # SOURCE3 517 6.5960 + angle_coeff @angle:cc-cd-cf harmonic 64.080 126.280 # SOURCE4 71 2.2936 + angle_coeff @angle:cc-cd-ch harmonic 64.920 126.050 # SOURCE4 30 1.4695 + angle_coeff @angle:cc-cd-cl harmonic 61.810 123.620 # SOURCE4 14 1.9282 + angle_coeff @angle:cc-cd-cy harmonic 63.930 122.130 # SOURCE4 10 0.8509 + angle_coeff @angle:c-cd-cd harmonic 63.720 122.690 # SOURCE3 2 0.0000 + angle_coeff @angle:c-cd-cf harmonic 63.000 123.100 # SOURCE4 5 2.3108 + angle_coeff @angle:cc-cd-h4 harmonic 47.190 129.110 # SOURCE3 418 3.1355 + angle_coeff @angle:cc-cd-ha harmonic 48.350 122.890 # SOURCE3 584 2.9334 + angle_coeff @angle:c-cd-cl harmonic 62.750 116.190 # SOURCE4 5 1.0839 + angle_coeff @angle:cc-cd-n harmonic 70.720 115.520 # SOURCE3 52 1.3322 + angle_coeff @angle:cc-cd-na harmonic 72.910 109.420 # SOURCE3 265 2.6051 + angle_coeff @angle:cc-cd-nc harmonic 69.420 123.820 # SOURCE4 14 0.3678 + angle_coeff @angle:cc-cd-nd harmonic 72.030 111.680 # SOURCE4 1078 1.9168 + angle_coeff @angle:cc-cd-nh harmonic 68.700 123.880 # SOURCE4 105 2.2114 + angle_coeff @angle:cc-cd-oh harmonic 69.540 123.710 # SOURCE4 47 1.3029 + angle_coeff @angle:cc-cd-os harmonic 69.960 120.300 # SOURCE3 64 5.4354 + angle_coeff @angle:cc-cd-ss harmonic 82.380 112.740 # SOURCE4 192 2.2341 + angle_coeff @angle:cc-cd-sy harmonic 76.890 124.690 # SOURCE4 22 0.6891 + angle_coeff @angle:cd-cd-cd harmonic 67.880 110.700 # SOURCE3 54 3.4091 + angle_coeff @angle:cd-cd-ce harmonic 65.800 122.560 # SOURCE4 38 1.7758 + angle_coeff @angle:cd-cd-cf harmonic 62.580 127.560 # SOURCE4 32 2.4879 + angle_coeff @angle:cd-cd-ch harmonic 63.320 127.380 # SOURCE4 21 0.9462 + angle_coeff @angle:cd-cd-cy harmonic 63.170 120.930 # SOURCE4 6 1.2205 + angle_coeff @angle:cd-cd-h4 harmonic 45.560 129.470 # SOURCE3 171 2.2734 + angle_coeff @angle:cd-cd-ha harmonic 47.020 121.510 # SOURCE4 1245 2.1421 + angle_coeff @angle:cd-cd-n2 harmonic 69.520 121.150 # SOURCE3 6 0.4642 + angle_coeff @angle:cd-cd-n harmonic 67.950 119.890 # SOURCE3 36 0.2095 + angle_coeff @angle:cd-cd-na harmonic 72.210 106.800 # SOURCE3 33 same_as_cc-cc-na + angle_coeff @angle:cd-cd-nc harmonic 71.150 112.560 # SOURCE3 141 4.2871 + angle_coeff @angle:cd-cd-nd harmonic 67.440 122.020 # SOURCE4 101 2.1232 + angle_coeff @angle:cd-cd-nh harmonic 68.260 120.050 # SOURCE4 86 1.2878 + angle_coeff @angle:cd-cd-oh harmonic 68.090 123.300 # SOURCE4 17 2.3237 + angle_coeff @angle:cd-cd-os harmonic 69.300 117.360 # SOURCE4 112 1.9292 + angle_coeff @angle:cd-cd-pc harmonic 63.840 115.360 # SOURCE3 84 3.2889 + angle_coeff @angle:cd-cd-ss harmonic 78.930 120.470 # SOURCE4 29 1.6911 + angle_coeff @angle:ce-cd-nd harmonic 68.130 124.900 # SOURCE4 5 2.3975 + angle_coeff @angle:cf-cd-na harmonic 66.090 124.600 # SOURCE4 8 1.6033 + angle_coeff @angle:cf-cd-nc harmonic 67.940 120.490 # SOURCE4 26 1.3524 + angle_coeff @angle:cf-cd-nd harmonic 66.910 121.180 # SOURCE4 29 1.3143 + angle_coeff @angle:cf-cd-os harmonic 68.380 117.800 # SOURCE4 7 1.1308 + angle_coeff @angle:cf-cd-ss harmonic 77.470 123.670 # SOURCE4 7 1.5823 + angle_coeff @angle:c-cd-h4 harmonic 46.770 118.190 # SOURCE4 8 0.2226 + angle_coeff @angle:c-cd-ha harmonic 46.990 117.020 # SOURCE3 56 1.9713 + angle_coeff @angle:cl-cd-nc harmonic 63.230 125.300 # SOURCE3 1 same_as_cl-cc-nd + angle_coeff @angle:c-cd-n2 harmonic 68.580 120.890 # SOURCE3 1 same_as_c-cc-n2 + angle_coeff @angle:c-cd-n harmonic 68.190 116.060 # SOURCE3 1 same_as_n-cc-c + angle_coeff @angle:c-cd-nc harmonic 67.450 121.860 # SOURCE4 46 2.4699 + angle_coeff @angle:c-cd-nd harmonic 64.310 130.800 # SOURCE3 1 0.0000 + angle_coeff @angle:c-cd-oh harmonic 69.870 114.020 # SOURCE4 18 0.9546 + angle_coeff @angle:c-cd-os harmonic 68.070 118.550 # SOURCE4 26 2.1350 + angle_coeff @angle:h4-cd-n harmonic 50.390 117.620 # SOURCE3 53 0.9721 + angle_coeff @angle:h4-cd-na harmonic 50.220 119.660 # SOURCE3 294 2.4702 + angle_coeff @angle:h4-cd-nc harmonic 51.390 119.110 # SOURCE3 135 1.6946 + angle_coeff @angle:h4-cd-nd harmonic 50.000 120.030 # SOURCE3 16 2.3863 + angle_coeff @angle:h4-cd-os harmonic 52.270 111.890 # SOURCE3 61 2.3500 + angle_coeff @angle:h4-cd-ss harmonic 54.360 117.750 # SOURCE3 40 3.1156 + angle_coeff @angle:h5-cd-n harmonic 50.820 115.830 # SOURCE4 10 0.2888 + angle_coeff @angle:h5-cd-na harmonic 49.760 122.100 # SOURCE3 16 1.4626 + angle_coeff @angle:h5-cd-nc harmonic 50.130 125.380 # SOURCE3 40 2.2157 + angle_coeff @angle:h5-cd-nd harmonic 49.290 123.700 # SOURCE3 6 0.3547 + angle_coeff @angle:h5-cd-os harmonic 51.300 116.330 # SOURCE3 12 3.2919 + angle_coeff @angle:h5-cd-ss harmonic 53.390 122.000 # SOURCE3 6 0.7237 + angle_coeff @angle:ha-cd-na harmonic 49.820 121.500 # SOURCE2 1 same_as_ha-cc-na + angle_coeff @angle:ha-cd-nc harmonic 51.410 118.880 # SOURCE3 20 2.8923 + angle_coeff @angle:ha-cd-nd harmonic 50.730 116.540 # SOURCE3 5 1.4482 + angle_coeff @angle:ha-cd-os harmonic 52.490 110.860 # SOURCE3 7 1.3846 + angle_coeff @angle:ha-cd-pc harmonic 42.350 121.760 # SOURCE3 84 2.2216 + angle_coeff @angle:ha-cd-ss harmonic 53.490 121.640 # SOURCE2 5 same_as_ha-cc-ss + angle_coeff @angle:na-cd-nc harmonic 74.780 112.020 # SOURCE3 17 2.2434 + angle_coeff @angle:na-cd-nd harmonic 70.890 121.040 # SOURCE4 62 1.4580 + angle_coeff @angle:na-cd-nh harmonic 72.430 116.980 # SOURCE4 46 1.4937 + angle_coeff @angle:na-cd-ss harmonic 84.890 111.460 # SOURCE4 20 0.8600 + angle_coeff @angle:nc-cd-nd harmonic 73.390 115.840 # SOURCE4 213 1.4060 + angle_coeff @angle:nc-cd-nh harmonic 72.410 120.110 # SOURCE3 5 0.9313 + angle_coeff @angle:nc-cd-oh harmonic 73.040 120.890 # SOURCE4 11 1.5340 + angle_coeff @angle:nc-cd-os harmonic 73.420 117.640 # SOURCE4 100 1.8409 + angle_coeff @angle:nc-cd-ss harmonic 84.180 114.510 # SOURCE3 8 0.3449 + angle_coeff @angle:nd-cd-nd harmonic 69.470 125.580 # SOURCE4 13 0.4672 + angle_coeff @angle:nd-cd-nh harmonic 72.140 117.470 # SOURCE4 23 1.5450 + angle_coeff @angle:nd-cd-ss harmonic 81.790 119.860 # SOURCE3 2 same_as_nc-cc-ss + angle_coeff @angle:nh-cd-nh harmonic 72.930 115.960 # SOURCE3 1 same_as_nh-cc-nh + angle_coeff @angle:nh-cd-os harmonic 73.160 116.070 # SOURCE4 12 0.5342 + angle_coeff @angle:nh-cd-ss harmonic 81.480 121.220 # SOURCE4 11 1.1514 + angle_coeff @angle:n-cd-na harmonic 70.500 122.010 # SOURCE4 13 1.2061 + angle_coeff @angle:n-cd-nc harmonic 70.990 123.410 # SOURCE4 88 0.9565 + angle_coeff @angle:n-cd-nd harmonic 69.060 126.700 # SOURCE4 54 0.3231 + angle_coeff @angle:n-cd-nh harmonic 72.210 116.880 # SOURCE4 47 0.3458 + angle_coeff @angle:n-cd-ss harmonic 80.730 122.890 # SOURCE4 7 1.1978 + angle_coeff @angle:oh-cd-os harmonic 75.470 111.610 # SOURCE4 6 1.1909 + angle_coeff @angle:os-cd-ss harmonic 78.460 132.010 # SOURCE3 1 same_as_os-cc-ss + angle_coeff @angle:ss-cd-ss harmonic 99.630 122.300 # SOURCE3 2 same_as_ss-cc-ss + angle_coeff @angle:ss-cd-sy harmonic 98.720 121.620 # SOURCE4 19 0.4931 + angle_coeff @angle:c2-ce-c3 harmonic 64.300 122.890 # SOURCE3 7 1.0449 + angle_coeff @angle:c2-ce-ca harmonic 65.160 123.080 # SOURCE3 6 2.1589 + angle_coeff @angle:c2-ce-cc harmonic 65.550 123.840 # SOURCE4 49 2.1264 + angle_coeff @angle:c2-ce-ce harmonic 65.730 123.080 # SOURCE3 12 0.6518 + angle_coeff @angle:c2-ce-cg harmonic 66.680 121.580 # SOURCE4 18 1.3663 + angle_coeff @angle:c2-ce-cl harmonic 62.220 119.510 # SOURCE4 24 1.4963 + angle_coeff @angle:c2-ce-h4 harmonic 48.640 125.580 # SOURCE4 11 0.9381 + angle_coeff @angle:c2-ce-ha harmonic 49.560 121.100 # SOURCE3 46 2.4054 + angle_coeff @angle:c2-ce-n1 harmonic 72.730 117.850 # SOURCE4 7 0.3180 + angle_coeff @angle:c2-ce-n2 harmonic 70.340 128.700 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-ce-na harmonic 69.290 119.190 # SOURCE4 5 0.8452 + angle_coeff @angle:c2-ce-ne harmonic 69.730 118.320 # SOURCE3 7 1.0468 + angle_coeff @angle:c2-ce-oh harmonic 70.180 123.780 # SOURCE4 10 1.8182 + angle_coeff @angle:c2-ce-p2 harmonic 61.560 118.240 # SOURCE3 1 + angle_coeff @angle:c2-ce-pe harmonic 61.300 118.760 # SOURCE3 8 2.3984 + angle_coeff @angle:c2-ce-px harmonic 60.970 119.720 # SOURCE3 6 0.5213 + angle_coeff @angle:c2-ce-py harmonic 61.150 122.130 # SOURCE3 5 3.1367 + angle_coeff @angle:c2-ce-sx harmonic 78.010 119.870 # SOURCE3 5 0.8557 + angle_coeff @angle:c2-ce-sy harmonic 78.410 120.350 # SOURCE3 5 0.5401 + angle_coeff @angle:c3-ce-ca harmonic 62.810 119.110 # SOURCE4 127 1.8824 + angle_coeff @angle:c3-ce-cc harmonic 63.490 118.180 # SOURCE4 22 1.7743 + angle_coeff @angle:c3-ce-ce harmonic 63.910 116.590 # SOURCE4 175 1.6539 + angle_coeff @angle:c3-ce-cf harmonic 64.510 122.180 # SOURCE4 119 2.0632 + angle_coeff @angle:c3-ce-cg harmonic 63.790 118.480 # SOURCE4 8 1.4756 + angle_coeff @angle:c3-ce-n2 harmonic 66.940 122.640 # SOURCE4 76 2.0781 + angle_coeff @angle:c3-ce-nf harmonic 67.240 120.750 # SOURCE4 6 2.1938 + angle_coeff @angle:c3-ce-nh harmonic 65.740 119.900 # SOURCE4 5 0.9634 + angle_coeff @angle:ca-ce-ca harmonic 63.870 117.820 # SOURCE4 100 0.9790 + angle_coeff @angle:ca-ce-cc harmonic 64.120 118.640 # SOURCE4 12 0.8455 + angle_coeff @angle:ca-ce-ce harmonic 63.840 119.620 # SOURCE4 14 1.9171 + angle_coeff @angle:ca-ce-cf harmonic 64.090 127.310 # SOURCE4 132 1.9691 + angle_coeff @angle:ca-ce-cl harmonic 62.350 114.220 # SOURCE4 6 1.3164 + angle_coeff @angle:ca-ce-h4 harmonic 46.710 116.860 # SOURCE4 74 0.9179 + angle_coeff @angle:ca-ce-ha harmonic 47.080 115.120 # SOURCE4 210 1.0763 + angle_coeff @angle:ca-ce-n2 harmonic 68.510 120.720 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-ce-nf harmonic 67.770 122.500 # SOURCE4 11 2.3863 + angle_coeff @angle:ca-ce-nh harmonic 67.850 115.510 # SOURCE4 93 0.9284 + angle_coeff @angle:ca-ce-oh harmonic 68.500 117.180 # SOURCE4 5 0.5951 + angle_coeff @angle:ca-ce-os harmonic 68.570 115.580 # SOURCE4 8 1.0735 + angle_coeff @angle:ca-ce-ss harmonic 77.470 117.730 # SOURCE4 5 1.1596 + angle_coeff @angle:c-ce-c2 harmonic 65.820 120.420 # SOURCE3 13 1.8877 + angle_coeff @angle:c-ce-c3 harmonic 63.430 116.630 # SOURCE4 169 2.4309 + angle_coeff @angle:c-ce-c harmonic 62.550 122.540 # SOURCE4 22 1.3987 + angle_coeff @angle:c-ce-ca harmonic 63.790 117.980 # SOURCE4 8 1.5129 + angle_coeff @angle:cc-ce-cd harmonic 63.280 130.360 # SOURCE4 5 2.3402 + angle_coeff @angle:cc-ce-cf harmonic 65.060 125.790 # SOURCE4 39 1.5227 + angle_coeff @angle:c-ce-cd harmonic 63.740 126.070 # SOURCE3 1 same_as_c-cf-cc + angle_coeff @angle:c-ce-ce harmonic 63.460 120.890 # SOURCE4 16 1.8719 + angle_coeff @angle:c-ce-cf harmonic 64.260 126.410 # SOURCE3 2 5.7847 + angle_coeff @angle:c-ce-cg harmonic 64.570 118.320 # SOURCE4 15 1.0595 + angle_coeff @angle:cc-ce-h4 harmonic 47.610 115.400 # SOURCE4 29 0.8744 + angle_coeff @angle:cc-ce-ha harmonic 47.630 115.360 # SOURCE4 66 0.9385 + angle_coeff @angle:c-ce-cl harmonic 62.010 115.400 # SOURCE4 6 1.0958 + angle_coeff @angle:cc-ce-n2 harmonic 68.910 121.690 # SOURCE4 52 2.2459 + angle_coeff @angle:cc-ce-nh harmonic 67.360 119.170 # SOURCE4 8 2.1378 + angle_coeff @angle:c-ce-cy harmonic 72.720 88.220 # SOURCE4 19 0.3234 + angle_coeff @angle:cd-ce-ce harmonic 65.140 122.940 # SOURCE4 6 0.3490 + angle_coeff @angle:cd-ce-ha harmonic 49.760 115.940 # SOURCE4 23 1.6379 + angle_coeff @angle:ce-ce-ce harmonic 64.550 118.740 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-ce-cf harmonic 65.490 124.050 # SOURCE4 166 1.7004 + angle_coeff @angle:ce-ce-cl harmonic 61.600 117.930 # SOURCE4 12 0.2639 + angle_coeff @angle:ce-ce-h4 harmonic 47.060 118.000 # SOURCE4 10 0.8551 + angle_coeff @angle:ce-ce-ha harmonic 47.500 115.900 # SOURCE3 12 0.4670 + angle_coeff @angle:ce-ce-n1 harmonic 66.840 127.150 # SOURCE3 2 same_as_cf-cf-n1 + angle_coeff @angle:ce-ce-n2 harmonic 68.520 123.000 # SOURCE3 2 0.0000 + angle_coeff @angle:ce-ce-oh harmonic 69.180 116.890 # SOURCE4 11 2.0380 + angle_coeff @angle:cf-ce-cg harmonic 66.060 123.940 # SOURCE4 21 1.4852 + angle_coeff @angle:cf-ce-cy harmonic 60.530 137.740 # SOURCE4 13 0.3952 + angle_coeff @angle:cf-ce-h4 harmonic 49.030 123.760 # SOURCE4 5 1.0909 + angle_coeff @angle:cf-ce-ha harmonic 50.180 118.290 # SOURCE4 299 1.3038 + angle_coeff @angle:cf-ce-n1 harmonic 72.090 120.030 # SOURCE4 6 1.9451 + angle_coeff @angle:cf-ce-n harmonic 72.630 108.180 # SOURCE4 54 0.5772 + angle_coeff @angle:cf-ce-nh harmonic 69.450 121.520 # SOURCE4 12 2.0106 + angle_coeff @angle:cf-ce-oh harmonic 70.830 121.620 # SOURCE4 12 0.5995 + angle_coeff @angle:cg-ce-cg harmonic 65.510 118.510 # SOURCE4 6 0.9614 + angle_coeff @angle:cg-ce-ha harmonic 47.910 116.610 # SOURCE4 12 0.3943 + angle_coeff @angle:cg-ce-n1 harmonic 69.540 119.500 # SOURCE2 1 0.0000 + angle_coeff @angle:cg-ce-n2 harmonic 69.590 121.430 # SOURCE4 6 0.8382 + angle_coeff @angle:c-ce-ha harmonic 46.590 117.260 # SOURCE3 11 2.7158 + angle_coeff @angle:c-ce-n harmonic 66.170 118.730 # SOURCE4 129 1.5548 + angle_coeff @angle:c-ce-nh harmonic 67.880 115.220 # SOURCE4 18 2.4886 + angle_coeff @angle:c-ce-oh harmonic 68.230 117.920 # SOURCE4 5 1.4580 + angle_coeff @angle:c-ce-os harmonic 69.050 113.780 # SOURCE4 21 1.8258 + angle_coeff @angle:h4-ce-n1 harmonic 52.650 116.360 # SOURCE4 7 0.2182 + angle_coeff @angle:h4-ce-n2 harmonic 52.370 121.520 # SOURCE4 105 1.2900 + angle_coeff @angle:h4-ce-ne harmonic 49.720 115.810 # SOURCE4 7 1.9836 + angle_coeff @angle:ha-ce-n1 harmonic 52.770 115.960 # SOURCE3 2 same_as_ha-cf-n1 + angle_coeff @angle:ha-ce-n2 harmonic 52.850 119.510 # SOURCE3 2 0.4623 + angle_coeff @angle:ha-ce-ne harmonic 49.160 118.590 # SOURCE3 5 1.1113 + angle_coeff @angle:ha-ce-nh harmonic 50.580 114.990 # SOURCE3 1 0.0000 + angle_coeff @angle:ha-ce-p2 harmonic 40.610 120.110 # SOURCE3 1 + angle_coeff @angle:ha-ce-pe harmonic 40.640 119.330 # SOURCE3 6 0.8966 + angle_coeff @angle:ha-ce-px harmonic 40.810 117.900 # SOURCE3 6 0.1809 + angle_coeff @angle:ha-ce-py harmonic 41.340 118.720 # SOURCE3 3 0.3064 + angle_coeff @angle:ha-ce-sx harmonic 52.960 115.450 # SOURCE3 3 0.6640 + angle_coeff @angle:ha-ce-sy harmonic 53.580 114.860 # SOURCE3 3 0.4717 + angle_coeff @angle:n2-ce-nh harmonic 71.550 124.860 # SOURCE4 83 2.0415 + angle_coeff @angle:n2-ce-os harmonic 74.520 118.130 # SOURCE4 6 0.1367 + angle_coeff @angle:n2-ce-ss harmonic 81.510 117.230 # SOURCE4 6 2.0518 + angle_coeff @angle:ne-ce-ne harmonic 68.070 123.870 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-ce-nh harmonic 71.870 112.910 # SOURCE4 12 1.1263 + angle_coeff @angle:nf-ce-nh harmonic 73.250 118.130 # SOURCE4 6 0.5842 + angle_coeff @angle:pe-ce-pe harmonic 57.690 129.790 # SOURCE3 1 0.0000 + angle_coeff @angle:py-ce-py harmonic 64.070 108.060 # SOURCE3 1 0.0000 + angle_coeff @angle:sx-ce-sx harmonic 97.090 120.320 # SOURCE3 1 0.0000 + angle_coeff @angle:sy-ce-sy harmonic 98.050 119.970 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-cf-c3 harmonic 64.300 122.890 # SOURCE3 7 same_as_c2-ce-c3 + angle_coeff @angle:c2-cf-ca harmonic 65.160 123.080 # SOURCE3 6 same_as_c2-ce-ca + angle_coeff @angle:c2-cf-cd harmonic 65.810 122.050 # SOURCE4 23 1.7894 + angle_coeff @angle:c2-cf-cf harmonic 65.730 123.080 # SOURCE3 12 same_as_c2-ce-ce + angle_coeff @angle:c2-cf-ch harmonic 66.510 122.220 # SOURCE3 3 same_as_c2-ce-cg + angle_coeff @angle:c2-cf-ha harmonic 49.560 121.100 # SOURCE3 46 same_as_c2-ce-ha + angle_coeff @angle:c2-cf-n2 harmonic 70.340 128.700 # SOURCE3 1 same_as_c2-ce-n2 + angle_coeff @angle:c2-cf-nf harmonic 69.730 118.320 # SOURCE3 7 same_as_c2-ce-ne + angle_coeff @angle:c2-cf-p2 harmonic 61.560 118.240 # SOURCE3 1 same_as_c2-ce-p2 + angle_coeff @angle:c2-cf-pf harmonic 61.300 118.760 # SOURCE3 8 same_as_c2-ce-pe + angle_coeff @angle:c2-cf-px harmonic 60.970 119.720 # SOURCE3 6 same_as_c2-ce-px + angle_coeff @angle:c2-cf-py harmonic 61.150 122.130 # SOURCE3 5 same_as_c2-ce-py + angle_coeff @angle:c2-cf-sx harmonic 78.010 119.870 # SOURCE3 5 same_as_c2-ce-sx + angle_coeff @angle:c2-cf-sy harmonic 78.410 120.350 # SOURCE3 5 same_as_c2-ce-sy + angle_coeff @angle:c3-cf-ca harmonic 62.650 119.700 # SOURCE4 51 1.2029 + angle_coeff @angle:c3-cf-cd harmonic 63.300 118.280 # SOURCE4 17 0.8680 + angle_coeff @angle:c3-cf-ce harmonic 64.550 122.030 # SOURCE4 102 1.9728 + angle_coeff @angle:c3-cf-cf harmonic 63.520 118.010 # SOURCE4 69 0.9443 + angle_coeff @angle:c3-cf-n2 harmonic 66.670 123.650 # SOURCE4 5 1.9155 + angle_coeff @angle:ca-cf-ca harmonic 64.500 115.530 # SOURCE4 12 0.5692 + angle_coeff @angle:ca-cf-cc harmonic 62.810 130.800 # SOURCE4 12 1.2696 + angle_coeff @angle:ca-cf-cd harmonic 64.490 116.650 # SOURCE4 5 0.8685 + angle_coeff @angle:ca-cf-ce harmonic 64.050 127.440 # SOURCE4 186 1.8735 + angle_coeff @angle:ca-cf-ha harmonic 47.060 115.210 # SOURCE4 135 0.9402 + angle_coeff @angle:ca-cf-n2 harmonic 68.510 120.720 # SOURCE3 1 same_as_ca-ce-n2 + angle_coeff @angle:ca-cf-ne harmonic 67.710 122.810 # SOURCE4 11 2.3913 + angle_coeff @angle:ca-cf-oh harmonic 69.220 115.690 # SOURCE4 6 0.8381 + angle_coeff @angle:c-cf-c2 harmonic 65.820 120.420 # SOURCE3 13 same_as_c-ce-c2 + angle_coeff @angle:c-cf-c3 harmonic 62.670 119.470 # SOURCE4 19 1.2665 + angle_coeff @angle:c-cf-c harmonic 63.510 118.850 # SOURCE3 1 same_as_c-ce-c + angle_coeff @angle:c-cf-cc harmonic 63.930 126.070 # SOURCE3 1 0.0000 + angle_coeff @angle:cc-cf-cf harmonic 64.530 126.040 # SOURCE4 6 1.0648 + angle_coeff @angle:c-cf-cd harmonic 64.140 117.760 # SOURCE4 10 1.2451 + angle_coeff @angle:c-cf-ce harmonic 64.260 126.410 # SOURCE3 2 same_as_c-ce-cf + angle_coeff @angle:cc-cf-ha harmonic 50.290 114.810 # SOURCE4 16 0.9788 + angle_coeff @angle:cd-cf-ce harmonic 64.650 126.530 # SOURCE4 49 2.0998 + angle_coeff @angle:cd-cf-ha harmonic 47.360 115.570 # SOURCE4 47 0.8973 + angle_coeff @angle:cd-cf-n2 harmonic 69.140 120.020 # SOURCE4 17 2.4566 + angle_coeff @angle:ce-cf-cf harmonic 65.420 124.330 # SOURCE4 175 1.6942 + angle_coeff @angle:ce-cf-ch harmonic 66.150 123.630 # SOURCE4 20 1.3910 + angle_coeff @angle:ce-cf-ha harmonic 50.240 117.980 # SOURCE4 356 1.4772 + angle_coeff @angle:ce-cf-n harmonic 72.320 108.630 # SOURCE4 10 1.2271 + angle_coeff @angle:ce-cf-oh harmonic 71.100 121.930 # SOURCE4 12 1.6250 + angle_coeff @angle:cf-cf-cf harmonic 64.550 118.740 # SOURCE3 1 same_as_ce-ce-ce + angle_coeff @angle:cf-cf-h4 harmonic 47.050 117.940 # SOURCE4 9 0.8559 + angle_coeff @angle:cf-cf-ha harmonic 47.500 115.900 # SOURCE3 12 0.4670 + angle_coeff @angle:cf-cf-n1 harmonic 66.650 127.150 # SOURCE3 2 2.1936 + angle_coeff @angle:cf-cf-n2 harmonic 69.760 118.660 # SOURCE4 11 1.2238 + angle_coeff @angle:c-cf-ha harmonic 46.590 117.260 # SOURCE3 11 2.7158 + angle_coeff @angle:ch-cf-ch harmonic 66.000 116.750 # SOURCE3 1 same_as_cg-ce-cg + angle_coeff @angle:ch-cf-ha harmonic 47.950 116.400 # SOURCE4 6 0.3381 + angle_coeff @angle:ch-cf-n1 harmonic 69.330 119.500 # SOURCE2 1 same_as_cg-ce-n1 + angle_coeff @angle:c-cf-n2 harmonic 70.160 114.880 # SOURCE4 5 1.3647 + angle_coeff @angle:c-cf-n harmonic 66.600 116.790 # SOURCE4 8 0.8255 + angle_coeff @angle:c-cf-nh harmonic 65.940 122.760 # SOURCE3 1 same_as_c-ce-nh + angle_coeff @angle:f-c-f harmonic 72.220 107.350 # SOURCE2 2 0.2500 + angle_coeff @angle:h4-cf-n2 harmonic 52.210 122.140 # SOURCE4 11 0.9297 + angle_coeff @angle:h4-cf-ne harmonic 52.280 120.210 # SOURCE4 6 0.8104 + angle_coeff @angle:ha-cf-n1 harmonic 52.480 115.960 # SOURCE3 2 3.5425 + angle_coeff @angle:ha-cf-n2 harmonic 52.850 119.510 # SOURCE3 2 same_as_ha-ce-n2 + angle_coeff @angle:ha-cf-nf harmonic 49.160 118.590 # SOURCE3 5 same_as_ha-ce-ne + angle_coeff @angle:ha-cf-nh harmonic 50.850 114.990 # SOURCE3 1 same_as_ha-ce-nh + angle_coeff @angle:ha-cf-p2 harmonic 40.610 120.110 # SOURCE3 1 same_as_ha-ce-p2 + angle_coeff @angle:ha-cf-pf harmonic 40.640 119.330 # SOURCE3 6 same_as_ha-ce-pe + angle_coeff @angle:ha-cf-px harmonic 40.810 117.900 # SOURCE3 6 same_as_ha-ce-px + angle_coeff @angle:ha-cf-py harmonic 41.340 118.720 # SOURCE3 3 same_as_ha-ce-py + angle_coeff @angle:ha-cf-sx harmonic 52.960 115.450 # SOURCE3 3 same_as_ha-ce-sx + angle_coeff @angle:ha-cf-sy harmonic 53.580 114.860 # SOURCE3 3 same_as_ha-ce-sy + angle_coeff @angle:n2-cf-nh harmonic 71.540 125.890 # SOURCE4 9 1.5587 + angle_coeff @angle:nf-cf-nf harmonic 68.070 123.870 # SOURCE3 1 same_as_ne-ce-ne + angle_coeff @angle:f-c-o harmonic 73.210 123.440 # SOURCE3 1 + angle_coeff @angle:pf-cf-pf harmonic 57.690 129.790 # SOURCE3 1 same_as_pe-ce-pe + angle_coeff @angle:py-cf-py harmonic 64.070 108.060 # SOURCE3 1 same_as_py-ce-py + angle_coeff @angle:f-c-s harmonic 80.250 124.000 # SOURCE2 1 0.0000 + angle_coeff @angle:sx-cf-sx harmonic 97.090 120.320 # SOURCE3 1 same_as_sx-ce-sx + angle_coeff @angle:sy-cf-sy harmonic 98.050 119.970 # SOURCE3 1 same_as_sy-ce-sy + angle_coeff @angle:c1-cg-ca harmonic 56.530 179.460 # SOURCE4 17 0.3461 + angle_coeff @angle:c1-cg-cc harmonic 56.970 178.600 # SOURCE4 6 0.3822 + angle_coeff @angle:c1-cg-ce harmonic 56.960 178.000 # SOURCE4 6 0.4324 + angle_coeff @angle:c1-cg-cg harmonic 58.180 179.660 # SOURCE4 16 0.1241 + angle_coeff @angle:c1-cg-ne harmonic 62.730 170.020 # SOURCE3 4 1.1724 + angle_coeff @angle:c1-cg-pe harmonic 56.730 173.290 # SOURCE3 11 4.9305 + angle_coeff @angle:ca-cg-ch harmonic 56.940 179.490 # SOURCE4 5 0.3022 + angle_coeff @angle:ca-cg-n1 harmonic 58.930 179.420 # SOURCE4 102 0.6923 + angle_coeff @angle:c-cg-c1 harmonic 56.190 179.140 # SOURCE3 2 0.0000 + angle_coeff @angle:cc-cg-n1 harmonic 59.440 178.460 # SOURCE4 24 0.7137 + angle_coeff @angle:ce-cg-ch harmonic 57.380 177.980 # SOURCE4 9 0.4223 + angle_coeff @angle:ce-cg-n1 harmonic 59.410 177.890 # SOURCE4 45 1.1337 + angle_coeff @angle:n1-cg-ne harmonic 65.040 174.070 # SOURCE4 14 1.2208 + angle_coeff @angle:h4-c-o harmonic 54.280 120.930 # SOURCE4 129 0.5769 + angle_coeff @angle:h5-c-n harmonic 52.390 112.190 # SOURCE4 33 0.4220 + angle_coeff @angle:h5-c-o harmonic 53.890 123.260 # SOURCE4 38 0.4806 + angle_coeff @angle:ha-c-ha harmonic 37.860 115.610 # SOURCE3 4 0.0458 + angle_coeff @angle:ha-c-i harmonic 36.710 110.580 # SOURCE3 1 0.0000 + angle_coeff @angle:ha-c-n harmonic 52.400 112.370 # SOURCE3 4 0.6424 + angle_coeff @angle:ha-c-o harmonic 54.270 121.940 # SOURCE3 51 2.3235 + angle_coeff @angle:ha-c-oh harmonic 53.970 111.820 # SOURCE3 4 1.9375 + angle_coeff @angle:ha-c-os harmonic 53.240 110.340 # SOURCE3 8 1.9344 + angle_coeff @angle:ha-c-s harmonic 56.030 119.560 # SOURCE3 3 0.7586 + angle_coeff @angle:c1-ch-ca harmonic 56.450 180.000 # SOURCE3 2 same_as_c1-cg-ca + angle_coeff @angle:c1-ch-cf harmonic 56.900 178.320 # SOURCE3 1 same_as_c1-cg-ce + angle_coeff @angle:c1-ch-ch harmonic 58.120 180.000 # SOURCE3 2 same_as_c1-cg-cg + angle_coeff @angle:c1-ch-nf harmonic 62.730 170.020 # SOURCE3 4 same_as_c1-cg-ne + angle_coeff @angle:c1-ch-pf harmonic 56.730 173.290 # SOURCE3 11 same_as_c1-cg-pe + angle_coeff @angle:ca-ch-cg harmonic 56.900 179.740 # SOURCE4 8 0.2890 + angle_coeff @angle:ca-ch-n1 harmonic 58.830 180.000 # SOURCE3 1 same_as_ca-cg-n1 + angle_coeff @angle:c-ch-c1 harmonic 56.190 179.140 # SOURCE3 2 same_as_c-cg-c1 + angle_coeff @angle:cd-ch-n1 harmonic 59.410 178.620 # SOURCE4 26 0.2919 + angle_coeff @angle:cf-ch-cg harmonic 57.400 177.900 # SOURCE4 8 0.4883 + angle_coeff @angle:cf-ch-n1 harmonic 59.370 178.120 # SOURCE4 22 1.5200 + angle_coeff @angle:cg-ch-ch harmonic 58.680 179.670 # SOURCE4 7 0.1439 + angle_coeff @angle:n1-ch-nf harmonic 64.660 176.170 # SOURCE2 3 same_as_n1-cg-ne + angle_coeff @angle:i-c-i harmonic 59.790 116.450 # SOURCE3 1 0.0000 + angle_coeff @angle:i-c-o harmonic 55.510 122.020 # SOURCE3 4 1.2961 + angle_coeff @angle:f-cl-f harmonic 50.000 87.500 # SOURCE2 1 estimated_force_constant + angle_coeff @angle:n2-c-n2 harmonic 71.830 110.310 # SOURCE3 1 + angle_coeff @angle:n2-c-o harmonic 73.020 122.500 # SOURCE3 1 + angle_coeff @angle:n4-c-n4 harmonic 64.710 114.640 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-c-o harmonic 69.580 118.830 # SOURCE3 4 3.8516 + angle_coeff @angle:nc-c-o harmonic 74.050 123.980 # SOURCE4 66 0.9502 + angle_coeff @angle:nd-c-o harmonic 73.720 121.760 # SOURCE4 55 1.1138 + angle_coeff @angle:ne-c-ne harmonic 73.220 110.310 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-c-o harmonic 72.940 126.030 # SOURCE4 39 0.9885 + angle_coeff @angle:nf-c-nf harmonic 73.070 110.310 # SOURCE3 1 same_as_ne-c-ne + angle_coeff @angle:nf-c-o harmonic 73.320 124.390 # SOURCE3 3 same_as_ne-c-o + angle_coeff @angle:n-c-n harmonic 74.800 113.380 # SOURCE4 635 1.4358 + angle_coeff @angle:n-c-nc harmonic 72.690 117.050 # SOURCE4 54 0.7020 + angle_coeff @angle:n-c-nd harmonic 71.900 117.060 # SOURCE4 23 0.9856 + angle_coeff @angle:n-c-ne harmonic 74.440 110.370 # SOURCE4 10 1.7492 + angle_coeff @angle:n-c-o harmonic 75.830 122.030 # SOURCE3 221 2.3565 + angle_coeff @angle:n-c-oh harmonic 76.220 113.630 # SOURCE4 5 1.1209 + angle_coeff @angle:no-c-no harmonic 66.540 109.280 # SOURCE3 1 + angle_coeff @angle:no-c-o harmonic 67.950 125.360 # SOURCE3 1 + angle_coeff @angle:n-c-os harmonic 76.680 109.280 # SOURCE4 318 0.8749 + angle_coeff @angle:n-c-s harmonic 83.180 123.880 # SOURCE3 5 1.2935 + angle_coeff @angle:n-c-sh harmonic 83.030 112.610 # SOURCE4 8 1.2601 + angle_coeff @angle:n-c-ss harmonic 84.610 110.420 # SOURCE4 59 1.5507 + angle_coeff @angle:oh-c-oh harmonic 78.910 110.560 # SOURCE3 2 0.5498 + angle_coeff @angle:oh-c-s harmonic 84.340 123.440 # SOURCE3 1 0.0000 + angle_coeff @angle:o-c-o harmonic 78.170 130.380 # SOURCE4 429 1.0315 + angle_coeff @angle:o-c-oh harmonic 77.380 122.880 # SOURCE3 33 2.1896 + angle_coeff @angle:o-c-os harmonic 75.930 123.330 # SOURCE4 1708 1.0632 + angle_coeff @angle:o-c-p2 harmonic 59.770 123.100 # SOURCE3 1 + angle_coeff @angle:o-c-p3 harmonic 60.900 120.790 # SOURCE3 1 + angle_coeff @angle:o-c-p5 harmonic 60.850 121.200 # SOURCE4 8 1.2117 + angle_coeff @angle:o-c-pe harmonic 59.440 123.020 # SOURCE3 3 0.1404 + angle_coeff @angle:o-c-pf harmonic 59.440 123.020 # SOURCE3 3 same_as_o-c-pe + angle_coeff @angle:o-c-px harmonic 60.640 119.100 # SOURCE3 1 0.0000 + angle_coeff @angle:o-c-py harmonic 61.200 121.710 # SOURCE4 5 0.3133 + angle_coeff @angle:o-c-s4 harmonic 77.510 121.150 # SOURCE3 1 + angle_coeff @angle:o-c-s6 harmonic 78.060 119.450 # SOURCE3 1 + angle_coeff @angle:o-c-s harmonic 86.330 120.440 # SOURCE3 2 0.0000 + angle_coeff @angle:o-c-sh harmonic 81.240 121.410 # SOURCE3 4 1.4052 + angle_coeff @angle:os-c-os harmonic 76.450 111.380 # SOURCE4 12 0.8309 + angle_coeff @angle:o-c-ss harmonic 81.780 122.290 # SOURCE3 7 1.9240 + angle_coeff @angle:os-c-s harmonic 83.310 125.030 # SOURCE4 18 0.9978 + angle_coeff @angle:os-c-ss harmonic 83.910 113.630 # SOURCE4 5 0.7367 + angle_coeff @angle:o-c-sx harmonic 76.880 121.150 # SOURCE3 5 3.6452 + angle_coeff @angle:o-c-sy harmonic 78.310 119.320 # SOURCE3 5 2.4495 + angle_coeff @angle:p2-c-p2 harmonic 58.960 113.750 # SOURCE3 1 + angle_coeff @angle:p3-c-p3 harmonic 58.400 118.040 # SOURCE3 1 0.0000 + angle_coeff @angle:p3-c-py harmonic 67.140 90.080 # SOURCE3 1 0.0000 + angle_coeff @angle:p5-c-p5 harmonic 57.080 123.760 # SOURCE3 1 + angle_coeff @angle:ca-cp-ca harmonic 67.250 118.330 # SOURCE4 521 0.6228 + angle_coeff @angle:ca-cp-cp harmonic 64.140 121.140 # SOURCE4 979 1.4462 + angle_coeff @angle:ca-cp-na harmonic 68.850 119.430 # SOURCE4 21 0.6591 + angle_coeff @angle:ca-cp-nb harmonic 69.270 121.650 # SOURCE4 63 0.6564 + angle_coeff @angle:cp-cp-cp harmonic 72.200 90.000 # SOURCE3 4 0.0000 + angle_coeff @angle:cp-cp-cq harmonic 62.640 124.480 # SOURCE4 5 1.9038 + angle_coeff @angle:cp-cp-nb harmonic 68.050 116.600 # SOURCE4 88 1.1887 + angle_coeff @angle:pe-c-pe harmonic 58.620 113.770 # SOURCE3 1 0.0000 + angle_coeff @angle:pf-c-pf harmonic 58.620 113.770 # SOURCE3 1 same_as_pe-c-pe + angle_coeff @angle:nb-cp-nb harmonic 71.310 125.720 # SOURCE4 5 0.6674 + angle_coeff @angle:py-c-py harmonic 57.520 123.800 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-cq-ca harmonic 67.000 118.240 # SOURCE4 5 0.2181 + angle_coeff @angle:ca-cq-cq harmonic 64.220 120.410 # SOURCE4 12 1.4029 + angle_coeff @angle:ca-cq-nb harmonic 69.270 121.650 # SOURCE4 63 same as ca-cp-nb + angle_coeff @angle:cp-cq-cq harmonic 62.640 124.470 # SOURCE4 5 1.0864 + angle_coeff @angle:cq-cq-cq harmonic 72.200 90.000 # SOURCE3 4 0.0000 + angle_coeff @angle:cq-cq-nb harmonic 68.050 116.600 # SOURCE4 88 same as cp-cp-nb + angle_coeff @angle:s4-c-s4 harmonic 98.110 108.810 # SOURCE3 1 + angle_coeff @angle:s6-c-s6 harmonic 95.130 115.750 # SOURCE3 1 + angle_coeff @angle:sh-c-sh harmonic 100.060 115.330 # SOURCE3 1 0.0000 + angle_coeff @angle:s-c-s harmonic 104.130 120.400 # SOURCE3 2 1.2766 + angle_coeff @angle:s-c-sh harmonic 99.770 122.760 # SOURCE4 11 1.5734 + angle_coeff @angle:s-c-ss harmonic 99.130 125.900 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-c-ss harmonic 102.180 113.000 # SOURCE3 1 0.0000 + angle_coeff @angle:sx-c-sx harmonic 97.340 108.800 # SOURCE3 1 0.0000 + angle_coeff @angle:sy-c-sy harmonic 95.370 115.780 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-cu-cx harmonic 58.560 148.210 # SOURCE4 6 1.8305 + angle_coeff @angle:c-cu-cu harmonic 94.970 62.600 # SOURCE2 1 0.0000 + angle_coeff @angle:cu-cu-cx harmonic 100.970 50.800 # SOURCE2 1 0.0000 + angle_coeff @angle:cu-cu-ha harmonic 46.110 147.730 # SOURCE2 3 2.0950 + angle_coeff @angle:cv-cv-cy harmonic 73.280 94.170 # SOURCE3 2 0.0000 + angle_coeff @angle:cv-cv-ha harmonic 47.300 133.700 # SOURCE3 2 0.0000 + angle_coeff @angle:cx-cv-cx harmonic 84.660 63.900 # SOURCE2 1 0.0000 + angle_coeff @angle:cy-cv-ha harmonic 42.890 132.140 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-cx-cx harmonic 63.100 120.660 # SOURCE4 9 0.9067 + angle_coeff @angle:c2-cx-cx harmonic 62.330 120.540 # SOURCE4 51 2.2377 + angle_coeff @angle:c2-cx-h1 harmonic 46.630 115.780 # SOURCE4 8 0.2332 + angle_coeff @angle:c2-cx-hc harmonic 46.770 115.100 # SOURCE4 12 0.7463 + angle_coeff @angle:c2-cx-os harmonic 67.140 116.170 # SOURCE4 14 1.2782 + angle_coeff @angle:c3-cx-c3 harmonic 63.000 114.480 # SOURCE4 46 1.9627 + angle_coeff @angle:c3-cx-cx harmonic 61.820 120.060 # SOURCE4 448 2.1467 + angle_coeff @angle:c3-cx-h1 harmonic 45.870 115.420 # SOURCE4 89 1.1096 + angle_coeff @angle:c3-cx-hc harmonic 46.120 114.160 # SOURCE4 85 1.1118 + angle_coeff @angle:c3-cx-n3 harmonic 64.310 118.500 # SOURCE4 17 2.4897 + angle_coeff @angle:c3-cx-os harmonic 66.570 115.500 # SOURCE4 161 1.3016 + angle_coeff @angle:ca-cx-cx harmonic 61.860 122.180 # SOURCE4 65 1.6898 + angle_coeff @angle:ca-cx-h1 harmonic 46.810 114.570 # SOURCE4 7 0.6498 + angle_coeff @angle:ca-cx-hc harmonic 47.050 113.410 # SOURCE4 18 0.7843 + angle_coeff @angle:ca-cx-oh harmonic 69.250 112.930 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-cx-os harmonic 66.420 118.500 # SOURCE4 6 0.7514 + angle_coeff @angle:c-cx-c3 harmonic 62.910 116.930 # SOURCE4 18 1.8253 + angle_coeff @angle:cc-cx-cx harmonic 63.040 118.970 # SOURCE4 30 0.7725 + angle_coeff @angle:cc-cx-hc harmonic 47.440 113.840 # SOURCE4 15 0.6682 + angle_coeff @angle:c-cx-cx harmonic 62.960 117.960 # SOURCE4 147 1.8483 + angle_coeff @angle:cd-cx-cx harmonic 62.450 120.460 # SOURCE4 9 0.8796 + angle_coeff @angle:c-cx-h1 harmonic 46.270 117.250 # SOURCE4 24 0.7935 + angle_coeff @angle:c-cx-hc harmonic 46.420 116.530 # SOURCE4 36 1.2830 + angle_coeff @angle:cl-cx-cl harmonic 62.910 114.200 # SOURCE2 1 0.0000 + angle_coeff @angle:cl-cx-cx harmonic 60.790 120.100 # SOURCE4 15 0.5917 + angle_coeff @angle:cl-cx-h1 harmonic 43.410 111.430 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-cx-hc harmonic 42.580 115.800 # SOURCE2 1 0.0000 + angle_coeff @angle:c-cx-os harmonic 67.250 115.590 # SOURCE4 36 0.8227 + angle_coeff @angle:cu-cx-cu harmonic 91.530 54.600 # SOURCE2 1 0.0000 + angle_coeff @angle:cu-cx-cx harmonic 88.720 58.500 # SOURCE4 7 0.1333 + angle_coeff @angle:cu-cx-hc harmonic 45.490 118.090 # SOURCE4 7 1.0126 + angle_coeff @angle:cx-cx-cx harmonic 87.900 60.000 # SOURCE4 681 0.6259 + angle_coeff @angle:cx-cx-cy harmonic 67.540 100.530 # SOURCE3 4 0.0000 + angle_coeff @angle:cx-cx-f harmonic 64.530 117.930 # SOURCE4 7 1.1613 + angle_coeff @angle:cx-cx-h1 harmonic 45.450 119.660 # SOURCE3 12 0.4529 + angle_coeff @angle:cx-cx-hc harmonic 45.790 117.920 # SOURCE3 92 1.1927 + angle_coeff @angle:cx-cx-hx harmonic 45.470 119.620 # SOURCE4 9 0.1118 + angle_coeff @angle:cx-cx-n3 harmonic 91.170 59.590 # SOURCE4 154 0.3104 + angle_coeff @angle:cx-cx-na harmonic 62.940 125.850 # SOURCE4 16 2.0385 + angle_coeff @angle:cx-cx-nh harmonic 92.030 59.150 # SOURCE4 116 0.6758 + angle_coeff @angle:cx-cx-os harmonic 93.610 59.070 # SOURCE4 306 0.5253 + angle_coeff @angle:cy-cx-hc harmonic 43.980 125.430 # SOURCE3 2 0.0000 + angle_coeff @angle:f-cx-f harmonic 70.610 106.900 # SOURCE2 2 1.4000 + angle_coeff @angle:f-cx-h1 harmonic 50.350 111.680 # SOURCE3 1 0.0000 + angle_coeff @angle:f-cx-hc harmonic 50.220 112.300 # SOURCE2 1 0.0000 + angle_coeff @angle:h1-cx-h1 harmonic 38.380 115.450 # SOURCE4 230 0.3302 + angle_coeff @angle:h1-cx-n3 harmonic 47.970 116.430 # SOURCE4 173 1.4531 + angle_coeff @angle:h1-cx-n harmonic 49.060 115.420 # SOURCE4 12 1.0443 + angle_coeff @angle:h1-cx-na harmonic 49.960 108.670 # SOURCE4 8 1.6134 + angle_coeff @angle:h1-cx-nh harmonic 48.500 116.320 # SOURCE4 151 1.0310 + angle_coeff @angle:h1-cx-os harmonic 50.010 115.170 # SOURCE3 8 0.0226 + angle_coeff @angle:h2-cx-h2 harmonic 37.870 119.430 # SOURCE3 1 0.0000 + angle_coeff @angle:h2-cx-n2 harmonic 47.550 117.180 # SOURCE3 4 0.0000 + angle_coeff @angle:hc-cx-hc harmonic 38.580 114.470 # SOURCE3 19 0.3295 + angle_coeff @angle:hc-cx-os harmonic 50.250 114.100 # SOURCE2 1 0.0000 + angle_coeff @angle:hx-cx-n4 harmonic 47.620 114.470 # SOURCE4 8 0.1059 + angle_coeff @angle:n2-cx-n2 harmonic 102.060 50.160 # SOURCE3 1 0.0000 + angle_coeff @angle:n-cx-oh harmonic 70.160 119.750 # SOURCE3 2 0.0000 + angle_coeff @angle:n-cx-os harmonic 92.710 65.980 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-cx-oh harmonic 76.670 107.850 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-cx-os harmonic 71.640 118.120 # SOURCE3 4 1.3581 + angle_coeff @angle:os-cx-os harmonic 70.900 115.840 # SOURCE4 7 2.0760 + angle_coeff @angle:c2-cy-cy harmonic 66.570 100.400 # SOURCE2 1 0.0000 + angle_coeff @angle:c3-cy-c3 harmonic 63.190 111.580 # SOURCE4 15 1.0060 + angle_coeff @angle:c3-cy-cy harmonic 60.760 118.700 # SOURCE4 293 1.8510 + angle_coeff @angle:c3-cy-h1 harmonic 46.160 111.770 # SOURCE4 119 0.4412 + angle_coeff @angle:c3-cy-hc harmonic 46.210 111.550 # SOURCE3 5 0.6276 + angle_coeff @angle:c3-cy-n3 harmonic 65.280 112.920 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-cy-n harmonic 68.320 104.050 # SOURCE4 122 0.5745 + angle_coeff @angle:c3-cy-os harmonic 66.990 111.960 # SOURCE4 11 1.0668 + angle_coeff @angle:c-cy-c3 harmonic 61.780 116.720 # SOURCE4 129 0.5236 + angle_coeff @angle:cc-cy-cy harmonic 60.440 121.790 # SOURCE4 6 0.2155 + angle_coeff @angle:c-cy-cy harmonic 71.810 84.990 # SOURCE4 263 0.6952 + angle_coeff @angle:cd-cy-cy harmonic 60.650 120.880 # SOURCE4 13 0.5333 + angle_coeff @angle:ce-cy-h2 harmonic 45.500 117.250 # SOURCE4 17 0.5351 + angle_coeff @angle:ce-cy-n harmonic 74.690 88.020 # SOURCE4 14 0.1416 + angle_coeff @angle:ce-cy-ss harmonic 74.010 121.330 # SOURCE4 13 0.1599 + angle_coeff @angle:c-cy-h1 harmonic 45.890 113.100 # SOURCE4 71 0.7655 + angle_coeff @angle:c-cy-hc harmonic 45.750 113.850 # SOURCE3 8 0.2067 + angle_coeff @angle:cl-cy-cy harmonic 61.910 112.000 # SOURCE3 2 0.0000 + angle_coeff @angle:cl-cy-h1 harmonic 44.060 106.590 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-cy-hc harmonic 42.600 114.000 # SOURCE2 1 0.0000 + angle_coeff @angle:c-cy-n harmonic 64.320 117.390 # SOURCE4 70 1.0742 + angle_coeff @angle:c-cy-os harmonic 66.270 114.420 # SOURCE4 6 1.2052 + angle_coeff @angle:cv-cy-cy harmonic 71.460 86.670 # SOURCE4 6 1.1600 + angle_coeff @angle:cv-cy-hc harmonic 46.060 114.470 # SOURCE4 7 0.4307 + angle_coeff @angle:cx-cy-cy harmonic 66.080 101.230 # SOURCE3 4 0.0000 + angle_coeff @angle:cx-cy-hc harmonic 45.250 118.300 # SOURCE2 3 5.7799 + angle_coeff @angle:cy-cy-cy harmonic 70.160 87.610 # SOURCE3 32 1.5407 + angle_coeff @angle:cy-cy-f harmonic 64.550 112.870 # SOURCE4 13 1.6772 + angle_coeff @angle:cy-cy-h1 harmonic 44.870 114.840 # SOURCE3 20 2.5651 + angle_coeff @angle:cy-cy-h2 harmonic 44.510 116.770 # SOURCE4 83 0.8683 + angle_coeff @angle:cy-cy-hc harmonic 44.820 115.140 # SOURCE3 114 0.8364 + angle_coeff @angle:cy-cy-n3 harmonic 73.470 87.580 # SOURCE3 4 0.6135 + angle_coeff @angle:cy-cy-n harmonic 65.220 112.130 # SOURCE3 31 2.0700 + angle_coeff @angle:cy-cy-na harmonic 63.370 119.700 # SOURCE4 9 0.3333 + angle_coeff @angle:cy-cy-oh harmonic 66.000 114.190 # SOURCE3 4 0.0000 + angle_coeff @angle:cy-cy-os harmonic 66.410 111.770 # SOURCE4 18 2.1334 + angle_coeff @angle:cy-cy-s6 harmonic 74.590 117.460 # SOURCE4 7 1.2423 + angle_coeff @angle:cy-cy-ss harmonic 74.450 118.180 # SOURCE4 55 0.9860 + angle_coeff @angle:h1-cy-h1 harmonic 39.010 109.720 # SOURCE3 6 0.8087 + angle_coeff @angle:h1-cy-n3 harmonic 48.210 113.360 # SOURCE3 6 1.4509 + angle_coeff @angle:h1-cy-n harmonic 49.100 111.180 # SOURCE4 141 0.5848 + angle_coeff @angle:h1-cy-oh harmonic 50.890 111.490 # SOURCE3 2 0.0000 + angle_coeff @angle:h1-cy-os harmonic 50.530 110.940 # SOURCE3 8 0.6522 + angle_coeff @angle:h1-cy-s6 harmonic 51.950 112.570 # SOURCE4 5 1.2943 + angle_coeff @angle:h2-cy-n harmonic 48.420 114.440 # SOURCE4 88 0.7114 + angle_coeff @angle:h2-cy-os harmonic 50.970 109.190 # SOURCE4 6 0.4162 + angle_coeff @angle:h2-cy-s6 harmonic 53.300 106.850 # SOURCE4 6 0.3975 + angle_coeff @angle:h2-cy-ss harmonic 52.700 109.730 # SOURCE4 92 0.7424 + angle_coeff @angle:hc-cy-hc harmonic 39.240 109.040 # SOURCE3 28 0.5962 + angle_coeff @angle:n-cy-os harmonic 71.620 107.500 # SOURCE4 9 2.3773 + angle_coeff @angle:n-cy-s6 harmonic 82.570 103.450 # SOURCE4 6 0.7197 + angle_coeff @angle:n-cy-ss harmonic 82.030 105.120 # SOURCE4 69 0.3987 + angle_coeff @angle:nh-cz-nh harmonic 72.970 120.170 # SOURCE4 26 0.3964 + angle_coeff @angle:br-n1-c1 harmonic 51.100 180.000 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-c1 harmonic 64.910 179.920 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-c2 harmonic 60.250 177.730 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-c3 harmonic 54.830 180.000 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-ca harmonic 56.970 179.990 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-cl harmonic 53.870 179.950 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-f harmonic 55.860 179.960 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-hn harmonic 45.620 179.980 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-i harmonic 46.230 179.950 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-n1 harmonic 66.890 180.000 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-n2 harmonic 65.700 171.560 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-n3 harmonic 60.690 175.590 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-n4 harmonic 59.680 179.690 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-na harmonic 59.950 180.000 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-nh harmonic 60.880 176.350 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-o harmonic 62.620 179.950 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-oh harmonic 62.880 174.310 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-os harmonic 62.150 176.610 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-p2 harmonic 53.810 172.830 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-p3 harmonic 54.260 173.510 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-p4 harmonic 53.620 173.640 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-p5 harmonic 56.480 177.280 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-s2 harmonic 76.360 178.110 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-s4 harmonic 69.870 169.600 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-s harmonic 67.470 179.990 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-s6 harmonic 78.230 175.920 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-sh harmonic 70.520 174.250 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-ss harmonic 70.160 176.060 # HF/6-31G* 1 + angle_coeff @angle:c2-n1-n1 harmonic 61.580 180.000 # HF/6-31G* 1 + angle_coeff @angle:c2-n1-o harmonic 73.090 116.940 # SOURCE3 2 0.0060 + angle_coeff @angle:c2-n1-s harmonic 81.900 118.000 # SOURCE3 2 0.0121 + angle_coeff @angle:c3-n1-n1 harmonic 56.300 180.000 # HF/6-31G* 1 + angle_coeff @angle:ca-n1-n1 harmonic 58.540 180.000 # HF/6-31G* 1 + angle_coeff @angle:ce-n1-o harmonic 71.350 122.400 # SOURCE3 1 same_as_cf-n1-o + angle_coeff @angle:ce-n1-s harmonic 82.090 117.340 # SOURCE3 1 same_as_cf-n1-s + angle_coeff @angle:cf-n1-o harmonic 71.060 122.400 # SOURCE3 1 0.0000 + angle_coeff @angle:cf-n1-s harmonic 81.960 117.340 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-n1-n1 harmonic 55.230 179.940 # HF/6-31G* 1 + angle_coeff @angle:f-n1-n1 harmonic 57.390 179.930 # HF/6-31G* 1 + angle_coeff @angle:hn-n1-n1 harmonic 47.140 179.910 # HF/6-31G* 1 + angle_coeff @angle:i-n1-n1 harmonic 47.260 179.940 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-n1 harmonic 68.970 179.970 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-n2 harmonic 67.650 171.570 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-n3 harmonic 62.490 175.090 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-n4 harmonic 61.310 179.910 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-na harmonic 61.630 179.970 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-nh harmonic 62.660 176.000 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-o harmonic 64.430 179.940 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-oh harmonic 64.780 173.770 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-os harmonic 64.010 176.120 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-p2 harmonic 54.850 174.710 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-p3 harmonic 55.500 174.270 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-s harmonic 69.160 180.000 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-n1-sh harmonic 72.150 175.070 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-ss harmonic 72.040 175.610 # HF/6-31G* 1 + angle_coeff @angle:o-n1-p2 harmonic 66.900 116.050 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-n1-s harmonic 80.340 119.930 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n2-br harmonic 63.890 106.600 # SOURCE3 1 + angle_coeff @angle:br-n2-c2 harmonic 59.130 112.400 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n2-n2 harmonic 61.080 110.420 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n2-o harmonic 60.100 114.470 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n2-p2 harmonic 63.250 111.030 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n2-s harmonic 78.980 115.780 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-n2-c1 harmonic 74.410 121.100 # SOURCE3 1 + angle_coeff @angle:c1-n2-c3 harmonic 58.670 151.880 # SOURCE3 4 15.8282 + angle_coeff @angle:c1-n2-cl harmonic 59.530 118.800 # SOURCE2 1 0.0000 + angle_coeff @angle:c1-n2-hn harmonic 51.470 126.500 # SOURCE2 3 7.6267 + angle_coeff @angle:c1-n2-n2 harmonic 76.750 113.400 # SOURCE3 1 + angle_coeff @angle:c1-n2-o harmonic 79.200 113.590 # SOURCE3 1 + angle_coeff @angle:c1-n2-p2 harmonic 66.970 119.570 # SOURCE3 1 + angle_coeff @angle:c1-n2-s harmonic 88.340 117.670 # SOURCE3 1 + angle_coeff @angle:c2-n2-c2 harmonic 70.760 118.180 # SOURCE3 1 + angle_coeff @angle:c2-n2-c3 harmonic 66.130 115.300 # SOURCE3 8 4.2940 + angle_coeff @angle:c2-n2-ca harmonic 69.830 119.940 # SOURCE3 1 + angle_coeff @angle:c2-n2-cl harmonic 60.950 112.640 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-n2-f harmonic 68.300 108.140 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-n2-hn harmonic 52.630 110.330 # SOURCE3 9 0.6498 + angle_coeff @angle:c2-n2-i harmonic 51.860 114.740 # SOURCE3 2 0.0139 + angle_coeff @angle:c2-n2-n1 harmonic 75.450 115.090 # HF/6-31G* 1 + angle_coeff @angle:c2-n2-n2 harmonic 77.940 103.590 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-n2-n3 harmonic 71.340 118.140 # SOURCE3 1 + angle_coeff @angle:c2-n2-n4 harmonic 62.390 112.220 # SOURCE3 3 0.0406 + angle_coeff @angle:c2-n2-n harmonic 70.160 117.980 # SOURCE4 11 0.9019 + angle_coeff @angle:c2-n2-na harmonic 70.350 117.580 # SOURCE3 8 1.6671 + angle_coeff @angle:c2-n2-nh harmonic 70.710 117.610 # SOURCE3 6 3.2642 + angle_coeff @angle:c2-n2-no harmonic 64.220 111.540 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-n2-o harmonic 75.470 116.940 # SOURCE3 1 + angle_coeff @angle:c2-n2-oh harmonic 72.080 110.890 # SOURCE4 22 1.2709 + angle_coeff @angle:c2-n2-os harmonic 71.830 110.510 # SOURCE4 13 0.7888 + angle_coeff @angle:c2-n2-p2 harmonic 67.180 116.000 # SOURCE3 1 + angle_coeff @angle:c2-n2-p3 harmonic 61.270 119.300 # SOURCE3 3 2.8489 + angle_coeff @angle:c2-n2-p4 harmonic 62.640 118.770 # SOURCE3 1 + angle_coeff @angle:c2-n2-s4 harmonic 86.210 112.290 # SOURCE3 1 + angle_coeff @angle:c2-n2-s6 harmonic 87.140 116.240 # SOURCE3 1 + angle_coeff @angle:c2-n2-s harmonic 86.900 118.000 # SOURCE3 1 + angle_coeff @angle:c2-n2-sh harmonic 79.840 115.480 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-n2-ss harmonic 82.230 118.040 # SOURCE3 4 2.2804 + angle_coeff @angle:c3-n2-c3 harmonic 63.760 110.700 # SOURCE3 1 + angle_coeff @angle:c3-n2-ca harmonic 65.970 114.950 # SOURCE4 5 0.9744 + angle_coeff @angle:c3-n2-ce harmonic 65.370 118.520 # SOURCE4 113 1.6475 + angle_coeff @angle:c3-n2-cf harmonic 65.320 118.690 # SOURCE4 10 1.2155 + angle_coeff @angle:c3-n2-hn harmonic 45.180 118.400 # SOURCE3 1 + angle_coeff @angle:c3-n2-n1 harmonic 68.640 116.200 # SOURCE4 12 0.5407 + angle_coeff @angle:c3-n2-n2 harmonic 69.290 111.180 # SOURCE3 7 0.4349 + angle_coeff @angle:c3-n2-nh harmonic 68.080 109.990 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n2-o harmonic 70.290 112.400 # SOURCE2 1 0.0000 + angle_coeff @angle:c3-n2-p2 harmonic 64.870 114.210 # SOURCE3 2 2.2772 + angle_coeff @angle:c3-n2-s6 harmonic 83.890 113.840 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n2-s harmonic 83.150 116.720 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-n2-ca harmonic 71.790 112.200 # SOURCE3 1 + angle_coeff @angle:ca-n2-hn harmonic 50.010 120.000 # SOURCE3 1 + angle_coeff @angle:ca-n2-n2 harmonic 74.000 113.530 # SOURCE3 1 + angle_coeff @angle:ca-n2-o harmonic 75.260 116.000 # SOURCE2 1 0.0000 + angle_coeff @angle:ca-n2-p2 harmonic 66.400 118.110 # SOURCE3 1 + angle_coeff @angle:ca-n2-s harmonic 85.850 120.110 # SOURCE3 1 + angle_coeff @angle:c-n2-c2 harmonic 66.220 120.970 # SOURCE3 1 + angle_coeff @angle:c-n2-c harmonic 62.710 123.800 # SOURCE3 1 + angle_coeff @angle:c-n2-ca harmonic 66.050 120.500 # SOURCE3 1 + angle_coeff @angle:cc-n2-cl harmonic 60.100 115.790 # SOURCE3 1 same_as_cd-n2-cl + angle_coeff @angle:cc-n2-hn harmonic 52.300 111.140 # SOURCE4 12 0.8109 + angle_coeff @angle:cc-n2-na harmonic 72.990 108.920 # SOURCE4 9 1.6245 + angle_coeff @angle:cc-n2-nh harmonic 70.350 118.470 # SOURCE4 6 1.7995 + angle_coeff @angle:cd-n2-cl harmonic 60.110 115.790 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n2-hn harmonic 52.630 110.090 # SOURCE4 8 0.6980 + angle_coeff @angle:ce-n2-hn harmonic 52.730 111.120 # SOURCE4 68 0.2440 + angle_coeff @angle:ce-n2-n harmonic 70.330 118.090 # SOURCE4 92 1.1048 + angle_coeff @angle:ce-n2-nh harmonic 70.640 118.550 # SOURCE4 52 1.1425 + angle_coeff @angle:ce-n2-o harmonic 77.370 112.160 # SOURCE3 1 + angle_coeff @angle:ce-n2-oh harmonic 71.450 113.480 # SOURCE4 36 1.7049 + angle_coeff @angle:ce-n2-os harmonic 71.290 112.780 # SOURCE4 33 0.8683 + angle_coeff @angle:ce-n2-s harmonic 87.710 116.280 # SOURCE3 1 + angle_coeff @angle:cf-n2-hn harmonic 53.860 106.500 # SOURCE3 1 same_as_ce-n2-hn + angle_coeff @angle:cf-n2-n harmonic 70.490 117.550 # SOURCE4 9 0.7822 + angle_coeff @angle:cf-n2-nh harmonic 70.490 119.080 # SOURCE3 2 same_as_ce-n2-nh + angle_coeff @angle:cf-n2-o harmonic 77.370 112.160 # SOURCE3 1 same_as_ce-n2-o + angle_coeff @angle:cf-n2-oh harmonic 72.610 109.870 # SOURCE3 1 same_as_ce-n2-oh + angle_coeff @angle:cf-n2-os harmonic 70.950 113.870 # SOURCE4 7 0.6449 + angle_coeff @angle:cf-n2-s harmonic 87.710 116.280 # SOURCE3 1 same_as_ce-n2-s + angle_coeff @angle:cl-n2-n1 harmonic 63.750 108.700 # SOURCE2 1 0.0000 + angle_coeff @angle:cl-n2-n2 harmonic 63.120 110.470 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-n2-o harmonic 62.610 114.030 # SOURCE3 1 + angle_coeff @angle:cl-n2-p2 harmonic 62.850 112.980 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-n2-s harmonic 79.610 115.770 # SOURCE3 1 0.0000 + angle_coeff @angle:cx-n2-n2 harmonic 90.460 64.920 # SOURCE3 2 0.0000 + angle_coeff @angle:f-n2-n2 harmonic 68.290 114.600 # SOURCE2 1 0.0000 + angle_coeff @angle:f-n2-o harmonic 71.170 110.100 # SOURCE2 1 0.0000 + angle_coeff @angle:f-n2-p2 harmonic 66.600 107.100 # SOURCE3 1 0.0000 + angle_coeff @angle:f-n2-s harmonic 84.970 110.730 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n2-hn harmonic 38.610 120.000 # SOURCE3 1 + angle_coeff @angle:hn-n2-n1 harmonic 55.330 114.100 # SOURCE2 1 0.0000 + angle_coeff @angle:hn-n2-n2 harmonic 55.840 105.010 # SOURCE3 19 1.5183 + angle_coeff @angle:hn-n2-ne harmonic 54.690 108.560 # SOURCE3 29 5.5708 + angle_coeff @angle:hn-n2-nf harmonic 54.690 108.560 # SOURCE3 29 same_as_hn-n2-ne + angle_coeff @angle:hn-n2-o harmonic 57.610 107.370 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n2-p2 harmonic 46.310 112.090 # SOURCE3 18 4.0663 + angle_coeff @angle:hn-n2-p4 harmonic 43.060 111.330 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n2-p5 harmonic 44.500 122.340 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n2-pe harmonic 48.420 111.410 # SOURCE3 20 4.9895 + angle_coeff @angle:hn-n2-pf harmonic 48.420 111.410 # SOURCE3 20 same_as_hn-n2-pe + angle_coeff @angle:hn-n2-s2 harmonic 61.190 115.800 # SOURCE2 1 0.0000 + angle_coeff @angle:hn-n2-s4 harmonic 58.650 111.210 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n2-s harmonic 62.150 108.170 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n2-s6 harmonic 60.520 112.590 # SOURCE3 2 0.0000 + angle_coeff @angle:i-n2-n2 harmonic 53.710 111.790 # SOURCE3 1 0.0000 + angle_coeff @angle:i-n2-o harmonic 52.330 116.820 # SOURCE3 1 0.0000 + angle_coeff @angle:i-n2-p2 harmonic 57.140 113.260 # SOURCE3 1 0.0000 + angle_coeff @angle:i-n2-s harmonic 71.310 116.850 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-n2-n1 harmonic 80.820 112.000 # HF/6-31G* 1 + angle_coeff @angle:n2-n2-n1 harmonic 62.280 180.000 # dac_for_azides 0 + angle_coeff @angle:n2-n2-n2 harmonic 78.200 109.490 # SOURCE3 2 0.0000 + angle_coeff @angle:n2-n2-n3 harmonic 76.590 108.880 # SOURCE3 1 + angle_coeff @angle:n2-n2-n4 harmonic 65.780 106.450 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-n2-na harmonic 74.180 112.230 # SOURCE3 1 + angle_coeff @angle:n2-n2-nh harmonic 74.760 111.700 # SOURCE3 5 0.3475 + angle_coeff @angle:n2-n2-no harmonic 67.680 105.970 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-n2-o harmonic 80.170 110.430 # SOURCE3 1 + angle_coeff @angle:n2-n2-oh harmonic 74.020 111.510 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-n2-os harmonic 74.690 108.380 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-n2-p2 harmonic 71.160 109.150 # SOURCE3 1 + angle_coeff @angle:n2-n2-p3 harmonic 64.580 113.050 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-n2-p4 harmonic 64.290 118.770 # SOURCE3 1 + angle_coeff @angle:n2-n2-p5 harmonic 70.950 110.460 # SOURCE3 1 + angle_coeff @angle:n2-n2-s4 harmonic 90.620 107.300 # SOURCE3 1 + angle_coeff @angle:n2-n2-s6 harmonic 91.570 111.250 # SOURCE3 1 + angle_coeff @angle:n2-n2-s harmonic 90.160 115.910 # SOURCE3 1 + angle_coeff @angle:n2-n2-sh harmonic 83.540 111.100 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-n2-ss harmonic 86.650 112.140 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-n2-n3 harmonic 72.950 115.070 # SOURCE3 1 + angle_coeff @angle:n3-n2-o harmonic 76.860 114.000 # SOURCE2 1 0.0000 + angle_coeff @angle:n3-n2-p2 harmonic 68.490 115.340 # SOURCE3 1 + angle_coeff @angle:n3-n2-s harmonic 88.540 117.130 # SOURCE3 1 + angle_coeff @angle:n4-n2-n4 harmonic 59.970 106.700 # SOURCE3 1 + angle_coeff @angle:n4-n2-o harmonic 64.860 112.200 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-n2-p2 harmonic 62.840 113.070 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-n2-s harmonic 79.030 118.500 # SOURCE3 1 0.0000 + angle_coeff @angle:na-n2-na harmonic 73.470 107.000 # SOURCE3 1 + angle_coeff @angle:na-n2-o harmonic 75.740 113.090 # SOURCE3 1 0.0000 + angle_coeff @angle:na-n2-p2 harmonic 66.830 119.160 # SOURCE3 1 0.0000 + angle_coeff @angle:na-n2-s harmonic 87.260 118.260 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-n2-nh harmonic 74.080 113.250 # SOURCE4 11 0.7711 + angle_coeff @angle:ne-n2-o harmonic 79.970 110.310 # SOURCE3 1 + angle_coeff @angle:ne-n2-s harmonic 89.910 116.220 # SOURCE3 1 + angle_coeff @angle:nf-n2-nh harmonic 74.690 111.380 # SOURCE3 1 same_as_ne-n2-nh + angle_coeff @angle:nf-n2-o harmonic 79.970 110.310 # SOURCE3 1 same_as_ne-n2-o + angle_coeff @angle:nf-n2-s harmonic 89.910 116.220 # SOURCE3 1 same_as_ne-n2-s + angle_coeff @angle:nh-n2-nh harmonic 69.670 121.200 # SOURCE3 1 + angle_coeff @angle:nh-n2-o harmonic 76.020 113.600 # SOURCE4 13 1.0945 + angle_coeff @angle:nh-n2-p2 harmonic 67.100 118.830 # SOURCE3 2 0.1024 + angle_coeff @angle:nh-n2-s harmonic 88.040 116.900 # SOURCE3 2 0.2276 + angle_coeff @angle:n-n2-n2 harmonic 75.480 108.180 # SOURCE4 8 0.3496 + angle_coeff @angle:n-n2-o harmonic 74.990 115.100 # SOURCE4 31 0.2796 + angle_coeff @angle:no-n2-no harmonic 62.810 103.700 # SOURCE3 1 + angle_coeff @angle:no-n2-o harmonic 70.400 100.760 # SOURCE3 1 0.0000 + angle_coeff @angle:no-n2-p2 harmonic 64.250 111.950 # SOURCE3 1 0.0000 + angle_coeff @angle:n-n2-p2 harmonic 67.320 117.300 # SOURCE3 1 0.0000 + angle_coeff @angle:n-n2-s harmonic 88.140 115.740 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-n2-oh harmonic 74.840 101.700 # SOURCE3 1 + angle_coeff @angle:oh-n2-p2 harmonic 67.990 115.110 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-n2-s harmonic 87.990 116.080 # SOURCE3 1 0.0000 + angle_coeff @angle:o-n2-o harmonic 81.020 115.370 # SOURCE3 1 + angle_coeff @angle:o-n2-oh harmonic 75.560 112.150 # SOURCE2 2 1.4500 + angle_coeff @angle:o-n2-os harmonic 75.730 110.350 # SOURCE3 2 0.0042 + angle_coeff @angle:o-n2-p2 harmonic 70.040 116.080 # SOURCE3 1 + angle_coeff @angle:o-n2-p3 harmonic 65.080 113.430 # SOURCE3 1 0.0000 + angle_coeff @angle:o-n2-p4 harmonic 67.340 110.610 # SOURCE3 1 + angle_coeff @angle:o-n2-p5 harmonic 72.480 109.110 # SOURCE3 1 + angle_coeff @angle:o-n2-pe harmonic 67.310 134.560 # SOURCE3 1 + angle_coeff @angle:o-n2-pf harmonic 67.310 134.560 # SOURCE3 1 same_as_o-n2-pe + angle_coeff @angle:o-n2-s4 harmonic 91.280 108.910 # SOURCE3 1 + angle_coeff @angle:o-n2-s6 harmonic 93.100 111.340 # SOURCE3 1 + angle_coeff @angle:o-n2-s harmonic 91.240 117.180 # SOURCE3 1 + angle_coeff @angle:o-n2-sh harmonic 82.970 114.980 # SOURCE3 1 0.0000 + angle_coeff @angle:os-n2-os harmonic 71.250 110.290 # SOURCE3 1 + angle_coeff @angle:os-n2-p2 harmonic 69.290 110.200 # SOURCE3 1 0.0000 + angle_coeff @angle:o-n2-ss harmonic 86.560 115.340 # SOURCE3 1 0.0000 + angle_coeff @angle:os-n2-s harmonic 89.190 112.230 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-n2-p2 harmonic 66.870 116.800 # SOURCE3 1 + angle_coeff @angle:p2-n2-p3 harmonic 61.450 124.480 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-n2-p4 harmonic 61.350 128.370 # SOURCE3 1 + angle_coeff @angle:p2-n2-p5 harmonic 65.160 123.470 # SOURCE3 1 + angle_coeff @angle:p2-n2-s4 harmonic 86.260 112.100 # SOURCE3 1 + angle_coeff @angle:p2-n2-s6 harmonic 86.440 115.700 # SOURCE3 1 + angle_coeff @angle:p2-n2-s harmonic 85.910 117.840 # SOURCE3 1 + angle_coeff @angle:p2-n2-sh harmonic 80.450 118.450 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-n2-ss harmonic 82.010 120.430 # SOURCE3 1 0.0000 + angle_coeff @angle:p3-n2-p3 harmonic 59.930 120.400 # SOURCE3 1 + angle_coeff @angle:p3-n2-s harmonic 80.080 120.860 # SOURCE3 1 0.0000 + angle_coeff @angle:p4-n2-s harmonic 77.830 131.840 # SOURCE3 1 + angle_coeff @angle:p5-n2-p5 harmonic 66.060 120.600 # SOURCE3 1 + angle_coeff @angle:p5-n2-s harmonic 85.340 119.890 # SOURCE3 1 + angle_coeff @angle:pe-n2-s harmonic 88.590 115.730 # SOURCE3 1 + angle_coeff @angle:pf-n2-s harmonic 88.590 115.730 # SOURCE3 1 same_as_pe-n2-s + angle_coeff @angle:s4-n2-s4 harmonic 105.720 119.180 # SOURCE3 1 + angle_coeff @angle:s4-n2-s6 harmonic 107.600 119.180 # SOURCE3 1 + angle_coeff @angle:s6-n2-s6 harmonic 109.720 119.180 # SOURCE3 1 + angle_coeff @angle:sh-n2-sh harmonic 96.030 123.930 # SOURCE3 1 + angle_coeff @angle:sh-n2-ss harmonic 98.240 123.930 # SOURCE3 1 + angle_coeff @angle:s-n2-s harmonic 109.670 120.880 # SOURCE3 1 + angle_coeff @angle:s-n2-s4 harmonic 110.840 113.000 # SOURCE3 1 + angle_coeff @angle:s-n2-s6 harmonic 109.880 119.610 # SOURCE3 1 + angle_coeff @angle:s-n2-sh harmonic 101.850 122.050 # SOURCE3 1 0.0000 + angle_coeff @angle:s-n2-ss harmonic 106.640 118.190 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-n2-ss harmonic 100.790 123.930 # SOURCE3 1 + angle_coeff @angle:br-n3-br harmonic 66.540 107.150 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n3-c3 harmonic 62.700 106.930 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-n3-c1 harmonic 64.090 123.340 # SOURCE3 1 + angle_coeff @angle:c1-n3-f harmonic 68.220 104.700 # SOURCE2 1 0.0000 + angle_coeff @angle:c1-n3-hn harmonic 47.740 118.310 # SOURCE3 1 + angle_coeff @angle:c1-n3-o harmonic 70.010 116.630 # SOURCE3 1 + angle_coeff @angle:c2-n3-c2 harmonic 66.220 124.680 # SOURCE3 1 + angle_coeff @angle:c2-n3-hn harmonic 49.110 119.380 # SOURCE3 1 + angle_coeff @angle:c3-n3-c3 harmonic 64.010 110.900 # SOURCE3 40 2.3048 + angle_coeff @angle:c3-n3-cl harmonic 62.170 107.230 # SOURCE3 3 0.3673 + angle_coeff @angle:c3-n3-cx harmonic 62.450 116.320 # SOURCE4 24 0.5119 + angle_coeff @angle:c3-n3-cy harmonic 61.690 118.260 # SOURCE4 14 0.8788 + angle_coeff @angle:c3-n3-f harmonic 66.810 103.130 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-n3-hn harmonic 47.130 109.920 # SOURCE3 120 2.2590 + angle_coeff @angle:c3-n3-i harmonic 56.980 108.480 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-n3-n2 harmonic 66.230 118.750 # SOURCE2 2 2.6500 + angle_coeff @angle:c3-n3-n3 harmonic 66.760 108.150 # SOURCE3 15 1.3999 + angle_coeff @angle:c3-n3-n4 harmonic 67.180 109.650 # SOURCE3 3 0.1146 + angle_coeff @angle:c3-n3-n harmonic 66.670 111.750 # SOURCE4 50 1.6777 + angle_coeff @angle:c3-n3-nh harmonic 66.370 111.890 # SOURCE4 21 1.3006 + angle_coeff @angle:c3-n3-no harmonic 66.020 111.270 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n3-o harmonic 68.680 113.310 # SOURCE3 5 8.9081 + angle_coeff @angle:c3-n3-oh harmonic 69.070 106.140 # SOURCE4 14 1.1040 + angle_coeff @angle:c3-n3-os harmonic 68.480 104.950 # SOURCE4 9 0.9687 + angle_coeff @angle:c3-n3-p3 harmonic 59.890 121.930 # SOURCE3 3 5.6009 + angle_coeff @angle:c3-n3-p5 harmonic 62.050 119.810 # SOURCE4 58 1.8367 + angle_coeff @angle:c3-n3-s4 harmonic 77.770 112.910 # SOURCE3 3 0.8983 + angle_coeff @angle:c3-n3-s6 harmonic 80.590 116.570 # SOURCE4 73 1.8772 + angle_coeff @angle:c3-n3-s harmonic 77.780 110.020 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n3-sh harmonic 78.550 112.700 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n3-ss harmonic 77.950 116.010 # SOURCE3 3 1.1944 + angle_coeff @angle:c3-n3-sy harmonic 79.010 115.270 # SOURCE4 108 1.7647 + angle_coeff @angle:cl-n3-cl harmonic 61.850 108.280 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-n3-hn harmonic 42.590 104.390 # SOURCE3 2 0.0000 + angle_coeff @angle:cl-n3-n3 harmonic 63.750 107.650 # SOURCE3 1 0.0000 + angle_coeff @angle:cx-n3-cx harmonic 86.390 60.710 # SOURCE4 57 0.2359 + angle_coeff @angle:cx-n3-hn harmonic 47.150 109.570 # SOURCE4 26 0.7439 + angle_coeff @angle:cx-n3-p5 harmonic 62.150 119.320 # SOURCE4 71 1.1948 + angle_coeff @angle:cx-n3-py harmonic 60.630 121.750 # SOURCE4 10 1.0295 + angle_coeff @angle:cy-n3-cy harmonic 70.040 90.870 # SOURCE4 10 0.5777 + angle_coeff @angle:cy-n3-hn harmonic 46.250 112.120 # SOURCE4 9 1.9058 + angle_coeff @angle:f-n3-f harmonic 67.710 102.220 # SOURCE2 4 0.7562 + angle_coeff @angle:f-n3-hn harmonic 50.780 99.800 # SOURCE2 1 0.0000 + angle_coeff @angle:hn-n3-hn harmonic 41.300 107.130 # SOURCE3 44 1.9687 + angle_coeff @angle:hn-n3-i harmonic 35.430 109.980 # SOURCE3 2 0.0000 + angle_coeff @angle:hn-n3-n1 harmonic 52.050 110.170 # HF/6-31G* 1 + angle_coeff @angle:hn-n3-n2 harmonic 51.400 115.940 # SOURCE3 1 + angle_coeff @angle:hn-n3-n3 harmonic 50.160 103.980 # SOURCE3 18 1.8593 + angle_coeff @angle:hn-n3-n4 harmonic 50.870 106.400 # SOURCE3 5 0.5863 + angle_coeff @angle:hn-n3-n harmonic 51.020 106.570 # SOURCE3 6 1.0767 + angle_coeff @angle:hn-n3-na harmonic 50.320 107.890 # SOURCE3 1 + angle_coeff @angle:hn-n3-nh harmonic 50.440 107.390 # SOURCE3 11 1.6294 + angle_coeff @angle:hn-n3-no harmonic 50.250 104.780 # SOURCE3 3 1.1126 + angle_coeff @angle:hn-n3-o harmonic 53.140 113.320 # SOURCE3 3 4.3945 + angle_coeff @angle:hn-n3-oh harmonic 53.080 101.110 # SOURCE3 4 0.9921 + angle_coeff @angle:hn-n3-os harmonic 51.670 100.920 # SOURCE3 6 0.7295 + angle_coeff @angle:hn-n3-p2 harmonic 42.850 120.260 # SOURCE3 1 + angle_coeff @angle:hn-n3-p3 harmonic 41.820 116.890 # SOURCE3 9 3.8816 + angle_coeff @angle:hn-n3-p4 harmonic 43.440 113.050 # SOURCE3 2 0.0000 + angle_coeff @angle:hn-n3-p5 harmonic 44.280 113.680 # SOURCE3 6 2.1781 + angle_coeff @angle:hn-n3-s4 harmonic 53.750 108.930 # SOURCE3 7 1.7819 + angle_coeff @angle:hn-n3-s harmonic 52.560 109.470 # SOURCE3 1 + angle_coeff @angle:hn-n3-s6 harmonic 58.300 109.330 # SOURCE4 86 0.9610 + angle_coeff @angle:hn-n3-sh harmonic 54.580 108.670 # SOURCE3 3 2.5025 + angle_coeff @angle:hn-n3-ss harmonic 54.880 109.850 # SOURCE3 5 2.3215 + angle_coeff @angle:hn-n3-sy harmonic 55.880 109.490 # SOURCE4 278 0.7897 + angle_coeff @angle:i-n3-i harmonic 60.040 111.270 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-n3-n1 harmonic 72.400 113.210 # HF/6-31G* 1 + angle_coeff @angle:n2-n3-n2 harmonic 71.820 118.730 # SOURCE3 1 + angle_coeff @angle:n2-n3-o harmonic 74.130 114.910 # SOURCE3 1 + angle_coeff @angle:n3-n3-n3 harmonic 69.570 105.710 # SOURCE3 3 0.3561 + angle_coeff @angle:n4-n3-n4 harmonic 69.040 113.480 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-n3-nh harmonic 70.910 107.140 # SOURCE3 1 + angle_coeff @angle:na-n3-na harmonic 69.210 112.000 # SOURCE3 1 + angle_coeff @angle:nh-n3-nh harmonic 70.750 107.150 # SOURCE3 1 0.0000 + angle_coeff @angle:n-n3-n harmonic 70.250 110.550 # SOURCE3 1 0.0000 + angle_coeff @angle:no-n3-no harmonic 67.040 115.260 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-n3-oh harmonic 72.790 107.180 # SOURCE3 1 0.0000 + angle_coeff @angle:o-n3-o harmonic 71.890 126.140 # SOURCE3 1 + angle_coeff @angle:o-n3-p2 harmonic 66.640 117.020 # SOURCE3 1 + angle_coeff @angle:o-n3-p4 harmonic 65.880 116.650 # SOURCE3 1 + angle_coeff @angle:o-n3-s4 harmonic 81.710 114.090 # SOURCE3 1 + angle_coeff @angle:o-n3-s6 harmonic 87.090 113.800 # SOURCE3 1 + angle_coeff @angle:o-n3-s harmonic 78.520 119.810 # SOURCE3 1 + angle_coeff @angle:os-n3-os harmonic 70.790 106.520 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-n3-p2 harmonic 60.890 130.130 # SOURCE3 1 + angle_coeff @angle:p3-n3-p3 harmonic 61.530 118.740 # SOURCE3 3 3.3755 + angle_coeff @angle:p4-n3-p4 harmonic 63.370 116.350 # SOURCE3 1 + angle_coeff @angle:p5-n3-p5 harmonic 63.830 119.420 # SOURCE3 1 0.0000 + angle_coeff @angle:s4-n3-s4 harmonic 96.310 120.020 # SOURCE3 1 0.0000 + angle_coeff @angle:s4-n3-s6 harmonic 99.300 120.950 # SOURCE3 1 + angle_coeff @angle:s6-n3-s6 harmonic 101.380 126.130 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-n3-sh harmonic 98.100 118.630 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-n3-ss harmonic 98.150 119.670 # SOURCE3 1 + angle_coeff @angle:s-n3-s harmonic 90.470 131.360 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-n3-ss harmonic 98.680 119.570 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n4-br harmonic 65.140 114.820 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n4-hn harmonic 41.380 108.440 # SOURCE3 7 0.5630 + angle_coeff @angle:c1-n4-c1 harmonic 65.530 113.870 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-n4-hn harmonic 48.620 110.190 # SOURCE3 7 1.0847 + angle_coeff @angle:c2-n4-c2 harmonic 63.010 112.580 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-n4-c3 harmonic 63.100 110.960 # SOURCE4 13 2.4632 + angle_coeff @angle:c2-n4-hn harmonic 46.430 111.360 # SOURCE3 13 1.2672 + angle_coeff @angle:c3-n4-c3 harmonic 62.840 110.640 # SOURCE3 13 1.3060 + angle_coeff @angle:c3-n4-ca harmonic 63.610 110.400 # SOURCE4 46 1.4643 + angle_coeff @angle:c3-n4-cc harmonic 62.840 111.090 # SOURCE4 7 0.7065 + angle_coeff @angle:c3-n4-cl harmonic 62.270 108.040 # SOURCE3 3 0.0000 + angle_coeff @angle:c3-n4-hn harmonic 46.190 110.110 # SOURCE3 100 1.3136 + angle_coeff @angle:c3-n4-n3 harmonic 66.730 108.720 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-n4-n4 harmonic 63.720 114.070 # SOURCE3 4 0.0000 + angle_coeff @angle:c3-n4-n harmonic 66.200 109.260 # SOURCE4 7 1.9859 + angle_coeff @angle:c3-n4-nh harmonic 64.760 111.730 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n4-no harmonic 65.250 109.080 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n4-o harmonic 67.250 111.660 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n4-oh harmonic 65.900 113.730 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n4-os harmonic 67.380 107.420 # SOURCE3 3 3.5920 + angle_coeff @angle:c3-n4-p2 harmonic 56.830 112.520 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n4-p3 harmonic 58.790 110.730 # SOURCE3 3 2.1084 + angle_coeff @angle:c3-n4-p5 harmonic 59.350 113.220 # SOURCE3 3 0.4021 + angle_coeff @angle:c3-n4-s4 harmonic 72.410 108.230 # SOURCE3 3 0.4195 + angle_coeff @angle:c3-n4-s6 harmonic 73.090 111.560 # SOURCE3 3 1.8851 + angle_coeff @angle:c3-n4-s harmonic 74.940 113.550 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n4-sh harmonic 74.840 115.810 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n4-ss harmonic 75.510 113.680 # SOURCE3 3 1.1405 + angle_coeff @angle:ca-n4-ca harmonic 63.210 114.480 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-n4-hn harmonic 47.540 108.520 # SOURCE3 5 1.1693 + angle_coeff @angle:c-n4-c harmonic 61.500 108.610 # SOURCE3 1 0.0000 + angle_coeff @angle:c-n4-hn harmonic 44.680 110.860 # SOURCE3 10 1.0073 + angle_coeff @angle:cl-n4-cl harmonic 60.960 114.910 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-n4-hn harmonic 42.500 108.870 # SOURCE3 7 0.7719 + angle_coeff @angle:f-n4-f harmonic 70.470 109.050 # SOURCE3 1 0.0000 + angle_coeff @angle:f-n4-hn harmonic 51.670 108.390 # SOURCE3 4 0.0000 + angle_coeff @angle:hn-n4-hn harmonic 40.520 108.110 # SOURCE3 208 1.4126 + angle_coeff @angle:hn-n4-i harmonic 36.440 108.720 # SOURCE3 7 1.2717 + angle_coeff @angle:hn-n4-n1 harmonic 51.790 109.390 # HF/6-31G* 1 + angle_coeff @angle:hn-n4-n2 harmonic 42.290 109.680 # SOURCE3 19 0.6266 + angle_coeff @angle:hn-n4-n3 harmonic 49.850 110.400 # SOURCE3 11 0.7307 + angle_coeff @angle:hn-n4-n4 harmonic 48.090 108.660 # SOURCE3 18 1.2967 + angle_coeff @angle:hn-n4-n harmonic 49.590 109.080 # SOURCE3 13 1.6047 + angle_coeff @angle:hn-n4-na harmonic 49.430 109.380 # SOURCE3 25 1.0758 + angle_coeff @angle:hn-n4-nh harmonic 48.360 109.920 # SOURCE3 12 0.7304 + angle_coeff @angle:hn-n4-no harmonic 49.190 104.380 # SOURCE3 2 0.0000 + angle_coeff @angle:hn-n4-o harmonic 52.090 109.260 # SOURCE3 6 2.1203 + angle_coeff @angle:hn-n4-oh harmonic 51.120 108.090 # SOURCE3 6 1.6728 + angle_coeff @angle:hn-n4-os harmonic 50.150 109.390 # SOURCE3 10 1.4403 + angle_coeff @angle:hn-n4-p2 harmonic 37.700 110.500 # SOURCE3 25 1.0664 + angle_coeff @angle:hn-n4-p3 harmonic 39.300 109.890 # SOURCE3 10 2.3870 + angle_coeff @angle:hn-n4-p4 harmonic 37.650 111.330 # SOURCE3 3 0.0000 + angle_coeff @angle:hn-n4-p5 harmonic 40.530 110.000 # SOURCE3 10 1.0282 + angle_coeff @angle:hn-n4-py harmonic 37.420 117.890 # SOURCE3 8 0.0000 + angle_coeff @angle:hn-n4-s4 harmonic 46.920 110.100 # SOURCE3 6 0.8471 + angle_coeff @angle:hn-n4-s harmonic 51.970 106.890 # SOURCE3 6 1.0775 + angle_coeff @angle:hn-n4-s6 harmonic 48.900 108.940 # SOURCE3 10 0.5715 + angle_coeff @angle:hn-n4-sh harmonic 52.260 108.560 # SOURCE3 6 0.8535 + angle_coeff @angle:hn-n4-ss harmonic 52.080 109.170 # SOURCE3 10 0.8455 + angle_coeff @angle:i-n4-i harmonic 58.990 118.490 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-n4-n1 harmonic 72.690 110.670 # HF/6-31G* 1 + angle_coeff @angle:n2-n4-n2 harmonic 59.430 108.640 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-n4-n3 harmonic 69.790 111.070 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-n4-n4 harmonic 65.210 115.490 # SOURCE3 1 0.0000 + angle_coeff @angle:na-n4-na harmonic 66.270 119.600 # SOURCE3 1 0.0000 + angle_coeff @angle:nh-n4-nh harmonic 67.830 109.380 # SOURCE3 1 0.0000 + angle_coeff @angle:n-n4-n harmonic 66.680 118.620 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-n4-oh harmonic 72.250 108.190 # SOURCE3 1 0.0000 + angle_coeff @angle:o-n4-o harmonic 70.280 120.970 # SOURCE3 1 0.0000 + angle_coeff @angle:os-n4-os harmonic 72.460 104.400 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-n4-p2 harmonic 55.970 113.910 # SOURCE3 2 0.0000 + angle_coeff @angle:p3-n4-p3 harmonic 56.000 121.380 # SOURCE3 1 0.0000 + angle_coeff @angle:p5-n4-p5 harmonic 61.270 107.020 # SOURCE3 1 0.0000 + angle_coeff @angle:py-n4-py harmonic 73.000 69.790 # SOURCE3 2 0.0000 + angle_coeff @angle:s4-n4-s4 harmonic 87.700 115.430 # SOURCE3 1 + angle_coeff @angle:s6-n4-s6 harmonic 92.770 109.510 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-n4-sh harmonic 96.690 112.590 # SOURCE3 1 0.0000 + angle_coeff @angle:s-n4-s harmonic 90.880 124.550 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-n4-ss harmonic 98.130 109.200 # SOURCE3 1 0.0000 + angle_coeff @angle:br-na-br harmonic 60.550 123.000 # SOURCE3 1 + angle_coeff @angle:br-na-c2 harmonic 63.610 100.480 # SOURCE3 2 1.0536 + angle_coeff @angle:br-na-ca harmonic 57.150 124.810 # SOURCE3 1 + angle_coeff @angle:br-na-cc harmonic 57.160 124.620 # SOURCE3 3 0.5348 + angle_coeff @angle:br-na-cd harmonic 57.160 124.620 # SOURCE3 3 same_as_br-na-cc + angle_coeff @angle:br-na-nc harmonic 59.860 119.420 # SOURCE3 4 1.6703 + angle_coeff @angle:br-na-nd harmonic 59.860 119.420 # SOURCE3 4 same_as_br-na-nc + angle_coeff @angle:br-na-os harmonic 63.920 104.990 # SOURCE3 1 0.0000 + angle_coeff @angle:br-na-p2 harmonic 59.980 121.010 # SOURCE3 1 + angle_coeff @angle:br-na-pc harmonic 60.360 120.260 # SOURCE3 3 2.1456 + angle_coeff @angle:br-na-pd harmonic 60.360 120.260 # SOURCE3 3 same_as_br-na-pc + angle_coeff @angle:br-na-ss harmonic 79.050 112.280 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-na-c1 harmonic 67.200 117.200 # SOURCE3 1 + angle_coeff @angle:c1-na-c2 harmonic 64.320 125.200 # SOURCE3 1 + angle_coeff @angle:c1-na-ca harmonic 66.540 120.570 # SOURCE3 1 + angle_coeff @angle:c1-na-cc harmonic 65.820 121.350 # SOURCE3 6 0.6517 + angle_coeff @angle:c1-na-cd harmonic 65.820 121.350 # SOURCE3 6 0.6517 + angle_coeff @angle:c1-na-nc harmonic 68.270 120.240 # SOURCE3 4 1.6849 + angle_coeff @angle:c1-na-nd harmonic 68.270 120.240 # SOURCE3 4 same_as_c1-na-nc + angle_coeff @angle:c1-na-os harmonic 70.240 106.960 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-na-p2 harmonic 60.440 122.250 # SOURCE3 1 + angle_coeff @angle:c1-na-pc harmonic 61.100 121.480 # SOURCE3 3 2.1681 + angle_coeff @angle:c1-na-pd harmonic 61.100 121.480 # SOURCE3 3 same_as_c1-na-pc + angle_coeff @angle:c1-na-ss harmonic 78.330 118.300 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-na-c2 harmonic 67.800 110.370 # SOURCE3 6 0.5121 + angle_coeff @angle:c2-na-c3 harmonic 64.230 117.200 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-na-ca harmonic 64.550 125.330 # SOURCE4 7 0.5648 + angle_coeff @angle:c2-na-cc harmonic 63.980 125.750 # SOURCE3 10 1.5856 + angle_coeff @angle:c2-na-cd harmonic 63.980 125.750 # SOURCE3 10 1.5856 + angle_coeff @angle:c2-na-cl harmonic 63.280 101.010 # SOURCE3 2 1.5799 + angle_coeff @angle:c2-na-f harmonic 68.640 103.110 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-na-hn harmonic 47.620 119.280 # SOURCE3 14 6.6027 + angle_coeff @angle:c2-na-i harmonic 58.980 106.740 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-na-n1 harmonic 66.270 124.810 # HF/6-31G* 1 + angle_coeff @angle:c2-na-n2 harmonic 65.800 125.000 # SOURCE3 1 + angle_coeff @angle:c2-na-n3 harmonic 64.640 124.800 # SOURCE3 1 + angle_coeff @angle:c2-na-n4 harmonic 65.190 121.320 # SOURCE3 1 + angle_coeff @angle:c2-na-n harmonic 65.630 124.700 # SOURCE3 1 + angle_coeff @angle:c2-na-na harmonic 65.140 124.600 # SOURCE3 1 + angle_coeff @angle:c2-na-nc harmonic 67.270 121.140 # SOURCE4 5 1.0225 + angle_coeff @angle:c2-na-nd harmonic 67.600 119.950 # SOURCE3 4 same_as_c2-na-nc + angle_coeff @angle:c2-na-nh harmonic 65.040 124.980 # SOURCE3 1 + angle_coeff @angle:c2-na-no harmonic 64.340 124.200 # SOURCE3 1 + angle_coeff @angle:c2-na-o harmonic 68.210 125.900 # SOURCE3 1 + angle_coeff @angle:c2-na-oh harmonic 65.800 123.900 # SOURCE3 1 + angle_coeff @angle:c2-na-os harmonic 68.530 110.330 # SOURCE3 4 3.2172 + angle_coeff @angle:c2-na-p2 harmonic 60.200 122.140 # SOURCE3 1 + angle_coeff @angle:c2-na-p3 harmonic 58.910 126.100 # SOURCE3 1 + angle_coeff @angle:c2-na-p4 harmonic 64.460 125.000 # SOURCE3 1 + angle_coeff @angle:c2-na-p5 harmonic 60.390 125.100 # SOURCE3 1 + angle_coeff @angle:c2-na-pc harmonic 60.800 121.560 # SOURCE3 3 1.6252 + angle_coeff @angle:c2-na-pd harmonic 60.800 121.560 # SOURCE3 3 same_as_c2-na-pc + angle_coeff @angle:c2-na-s4 harmonic 73.870 124.900 # SOURCE3 1 + angle_coeff @angle:c2-na-s6 harmonic 76.240 124.400 # SOURCE3 1 + angle_coeff @angle:c2-na-s harmonic 74.540 125.800 # SOURCE3 1 + angle_coeff @angle:c2-na-sh harmonic 76.230 125.100 # SOURCE3 1 + angle_coeff @angle:c2-na-ss harmonic 78.900 115.530 # SOURCE3 5 1.4036 + angle_coeff @angle:c3-na-c3 harmonic 60.720 125.590 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-na-ca harmonic 63.150 124.360 # SOURCE3 5 4.2557 + angle_coeff @angle:c3-na-cc harmonic 62.560 125.090 # SOURCE3 18 1.2138 + angle_coeff @angle:c3-na-cd harmonic 62.560 125.090 # SOURCE3 18 1.2138 + angle_coeff @angle:c3-na-cp harmonic 63.760 119.460 # SOURCE4 7 0.4108 + angle_coeff @angle:c3-na-n2 harmonic 65.480 120.050 # SOURCE4 5 0.8795 + angle_coeff @angle:c3-na-n harmonic 67.370 112.680 # SOURCE4 12 0.5122 + angle_coeff @angle:c3-na-nc harmonic 65.740 120.460 # SOURCE3 8 2.1625 + angle_coeff @angle:c3-na-nd harmonic 65.740 120.460 # SOURCE3 8 2.1625 + angle_coeff @angle:c3-na-os harmonic 68.910 104.390 # SOURCE3 3 1.2017 + angle_coeff @angle:c3-na-p2 harmonic 59.290 123.120 # SOURCE3 1 + angle_coeff @angle:c3-na-pc harmonic 59.960 122.110 # SOURCE3 3 2.8504 + angle_coeff @angle:c3-na-pd harmonic 59.960 122.110 # SOURCE3 3 same_as_c3-na-pc + angle_coeff @angle:c3-na-sh harmonic 80.220 110.280 # SOURCE3 1 + angle_coeff @angle:c3-na-ss harmonic 79.610 110.870 # SOURCE3 3 0.8260 + angle_coeff @angle:ca-na-ca harmonic 66.980 120.090 # SOURCE4 321 1.7366 + angle_coeff @angle:ca-na-cc harmonic 68.460 113.150 # SOURCE3 18 9.8644 + angle_coeff @angle:ca-na-cd harmonic 68.460 113.150 # SOURCE3 18 9.8644 + angle_coeff @angle:ca-na-cl harmonic 57.170 124.790 # SOURCE3 1 + angle_coeff @angle:ca-na-cp harmonic 65.880 120.960 # SOURCE4 20 1.2820 + angle_coeff @angle:ca-na-cx harmonic 63.070 124.090 # SOURCE4 12 1.8167 + angle_coeff @angle:ca-na-f harmonic 65.510 116.400 # SOURCE3 1 + angle_coeff @angle:ca-na-hn harmonic 47.630 125.590 # SOURCE4 437 1.1893 + angle_coeff @angle:ca-na-i harmonic 55.210 121.620 # SOURCE3 1 + angle_coeff @angle:ca-na-n2 harmonic 68.210 119.850 # SOURCE4 6 1.2043 + angle_coeff @angle:ca-na-n4 harmonic 66.370 120.190 # SOURCE3 1 + angle_coeff @angle:ca-na-n harmonic 67.340 122.000 # SOURCE3 1 + angle_coeff @angle:ca-na-na harmonic 66.290 123.760 # SOURCE3 1 + angle_coeff @angle:ca-na-nb harmonic 68.180 122.160 # SOURCE4 7 0.8543 + angle_coeff @angle:ca-na-nc harmonic 69.270 117.850 # SOURCE3 6 3.6536 + angle_coeff @angle:ca-na-nd harmonic 69.270 117.850 # SOURCE3 6 same_as_ca-na-nc + angle_coeff @angle:ca-na-nh harmonic 66.140 124.330 # SOURCE4 7 1.3855 + angle_coeff @angle:ca-na-o harmonic 71.140 119.990 # SOURCE4 51 1.2671 + angle_coeff @angle:ca-na-oh harmonic 66.690 124.080 # SOURCE3 1 + angle_coeff @angle:ca-na-os harmonic 69.700 109.460 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-na-p2 harmonic 59.660 125.850 # SOURCE3 1 + angle_coeff @angle:ca-na-p3 harmonic 59.650 124.380 # SOURCE3 1 + angle_coeff @angle:ca-na-p4 harmonic 65.120 124.970 # SOURCE3 1 + angle_coeff @angle:ca-na-p5 harmonic 61.240 123.300 # SOURCE3 1 + angle_coeff @angle:ca-na-pc harmonic 61.050 122.130 # SOURCE3 3 2.2393 + angle_coeff @angle:ca-na-pd harmonic 61.050 122.130 # SOURCE3 3 same_as_ca-na-pc + angle_coeff @angle:ca-na-py harmonic 57.370 140.880 # SOURCE3 2 0.0000 + angle_coeff @angle:ca-na-s4 harmonic 76.640 117.230 # SOURCE3 1 + angle_coeff @angle:ca-na-s6 harmonic 77.900 120.690 # SOURCE3 1 + angle_coeff @angle:ca-na-s harmonic 75.010 125.640 # SOURCE3 1 + angle_coeff @angle:ca-na-sh harmonic 76.630 125.440 # SOURCE3 1 + angle_coeff @angle:ca-na-ss harmonic 74.880 129.910 # SOURCE4 8 0.1449 + angle_coeff @angle:cc-na-cc harmonic 68.940 109.900 # SOURCE3 109 1.5547 + angle_coeff @angle:cc-na-cd harmonic 63.880 128.010 # SOURCE3 1 0.0000 + angle_coeff @angle:cc-na-ce harmonic 63.050 126.610 # SOURCE4 8 0.5158 + angle_coeff @angle:cc-na-cl harmonic 57.100 124.610 # SOURCE3 3 0.5208 + angle_coeff @angle:cc-na-f harmonic 64.600 118.030 # SOURCE3 4 0.3081 + angle_coeff @angle:cc-na-hn harmonic 46.990 125.660 # SOURCE4 549 1.5224 + angle_coeff @angle:cc-na-i harmonic 54.340 125.700 # SOURCE3 6 0.7821 + angle_coeff @angle:cc-na-n2 harmonic 66.830 122.960 # SOURCE3 15 0.9350 + angle_coeff @angle:cc-na-n4 harmonic 65.900 120.310 # SOURCE3 10 3.4394 + angle_coeff @angle:cc-na-n harmonic 66.520 123.190 # SOURCE3 13 0.3010 + angle_coeff @angle:cc-na-na harmonic 65.910 123.430 # SOURCE3 23 0.2088 + angle_coeff @angle:cc-na-nc harmonic 70.180 113.020 # SOURCE3 38 2.2867 + angle_coeff @angle:cc-na-nd harmonic 66.370 126.350 # SOURCE4 94 1.1249 + angle_coeff @angle:cc-na-nh harmonic 66.230 122.250 # SOURCE3 19 0.2010 + angle_coeff @angle:cc-na-no harmonic 65.400 121.780 # SOURCE3 9 0.3521 + angle_coeff @angle:cc-na-o harmonic 69.010 125.210 # SOURCE3 10 0.0124 + angle_coeff @angle:cc-na-oh harmonic 66.670 122.380 # SOURCE3 10 0.1570 + angle_coeff @angle:cc-na-os harmonic 67.340 115.740 # SOURCE3 41 5.4093 + angle_coeff @angle:cc-na-p2 harmonic 59.490 125.860 # SOURCE3 14 2.2993 + angle_coeff @angle:cc-na-p3 harmonic 59.280 125.250 # SOURCE3 8 0.1998 + angle_coeff @angle:cc-na-p4 harmonic 64.080 127.730 # SOURCE3 7 3.6077 + angle_coeff @angle:cc-na-p5 harmonic 60.690 124.700 # SOURCE3 13 1.4225 + angle_coeff @angle:cc-na-s4 harmonic 75.240 121.030 # SOURCE3 10 0.5589 + angle_coeff @angle:cc-na-s6 harmonic 77.180 122.190 # SOURCE3 10 0.9634 + angle_coeff @angle:cc-na-s harmonic 74.800 125.660 # SOURCE3 8 0.1880 + angle_coeff @angle:cc-na-sh harmonic 76.830 123.960 # SOURCE3 10 0.3424 + angle_coeff @angle:cc-na-ss harmonic 76.340 124.220 # SOURCE4 8 0.1585 + angle_coeff @angle:cd-na-cd harmonic 68.940 109.900 # SOURCE3 109 1.5547 + angle_coeff @angle:cd-na-cl harmonic 57.100 124.610 # SOURCE3 3 same_as_cc-na-cl + angle_coeff @angle:cd-na-f harmonic 64.600 118.030 # SOURCE3 4 0.3081 + angle_coeff @angle:cd-na-hn harmonic 47.070 125.220 # SOURCE4 312 1.1426 + angle_coeff @angle:cd-na-i harmonic 54.340 125.700 # SOURCE3 6 0.7821 + angle_coeff @angle:cd-na-n2 harmonic 66.830 122.960 # SOURCE3 15 0.9350 + angle_coeff @angle:cd-na-n4 harmonic 65.900 120.310 # SOURCE3 10 3.4394 + angle_coeff @angle:cd-na-n harmonic 66.520 123.190 # SOURCE3 13 0.3010 + angle_coeff @angle:cd-na-na harmonic 65.910 123.430 # SOURCE3 23 0.2088 + angle_coeff @angle:cd-na-nc harmonic 66.510 125.820 # SOURCE4 30 1.6776 + angle_coeff @angle:cd-na-nd harmonic 70.180 113.020 # SOURCE3 38 2.2867 + angle_coeff @angle:cd-na-nh harmonic 66.230 122.250 # SOURCE3 19 0.2010 + angle_coeff @angle:cd-na-no harmonic 65.400 121.780 # SOURCE3 9 0.3521 + angle_coeff @angle:cd-na-o harmonic 69.010 125.210 # SOURCE3 10 0.0124 + angle_coeff @angle:cd-na-oh harmonic 66.670 122.380 # SOURCE3 10 0.1570 + angle_coeff @angle:cd-na-os harmonic 65.210 123.420 # SOURCE4 7 2.3824 + angle_coeff @angle:cd-na-p2 harmonic 59.490 125.860 # SOURCE3 14 2.2993 + angle_coeff @angle:cd-na-p3 harmonic 59.280 125.250 # SOURCE3 8 0.1998 + angle_coeff @angle:cd-na-p4 harmonic 64.080 127.730 # SOURCE3 7 same_as_cc-na-p4 + angle_coeff @angle:cd-na-p5 harmonic 60.690 124.700 # SOURCE3 13 1.4225 + angle_coeff @angle:cd-na-s4 harmonic 75.240 121.030 # SOURCE3 10 0.5589 + angle_coeff @angle:cd-na-s6 harmonic 77.180 122.190 # SOURCE3 10 0.9634 + angle_coeff @angle:cd-na-s harmonic 74.800 125.660 # SOURCE3 8 0.1880 + angle_coeff @angle:cd-na-sh harmonic 76.830 123.960 # SOURCE3 10 0.3424 + angle_coeff @angle:cd-na-ss harmonic 77.930 119.180 # SOURCE3 36 5.0538 + angle_coeff @angle:cl-na-cl harmonic 56.330 122.800 # SOURCE3 1 + angle_coeff @angle:cl-na-nc harmonic 59.890 119.360 # SOURCE3 4 1.7128 + angle_coeff @angle:cl-na-nd harmonic 59.890 119.360 # SOURCE3 4 same_as_cl-na-nc + angle_coeff @angle:cl-na-os harmonic 63.040 106.580 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-na-p2 harmonic 58.340 121.290 # SOURCE3 1 + angle_coeff @angle:cl-na-pc harmonic 58.780 120.510 # SOURCE3 3 2.1985 + angle_coeff @angle:cl-na-pd harmonic 58.780 120.510 # SOURCE3 3 same_as_cl-na-pc + angle_coeff @angle:cl-na-ss harmonic 77.180 111.910 # SOURCE3 1 0.0000 + angle_coeff @angle:f-na-f harmonic 62.220 120.200 # SOURCE3 1 + angle_coeff @angle:f-na-nc harmonic 66.640 118.050 # SOURCE3 4 1.7931 + angle_coeff @angle:f-na-nd harmonic 66.640 118.050 # SOURCE3 4 same_as_f-na-nc + angle_coeff @angle:f-na-os harmonic 69.150 103.860 # SOURCE3 1 0.0000 + angle_coeff @angle:f-na-p2 harmonic 59.680 119.950 # SOURCE3 1 + angle_coeff @angle:f-na-pc harmonic 60.340 119.100 # SOURCE3 3 2.3967 + angle_coeff @angle:f-na-pd harmonic 60.340 119.100 # SOURCE3 3 same_as_f-na-pc + angle_coeff @angle:f-na-ss harmonic 80.160 108.010 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-na-hn harmonic 39.830 116.800 # SOURCE3 1 + angle_coeff @angle:hn-na-n harmonic 50.900 111.260 # SOURCE4 5 1.1280 + angle_coeff @angle:hn-na-nc harmonic 50.000 119.610 # SOURCE3 16 1.8079 + angle_coeff @angle:hn-na-nd harmonic 50.000 119.610 # SOURCE3 16 1.8079 + angle_coeff @angle:hn-na-os harmonic 51.440 101.410 # SOURCE3 7 3.0814 + angle_coeff @angle:hn-na-p2 harmonic 40.320 122.520 # SOURCE3 1 + angle_coeff @angle:hn-na-pc harmonic 40.940 121.480 # SOURCE3 3 2.9355 + angle_coeff @angle:hn-na-pd harmonic 40.940 121.480 # SOURCE3 3 same_as_hn-na-pc + angle_coeff @angle:hn-na-ss harmonic 53.460 113.950 # SOURCE3 1 0.0000 + angle_coeff @angle:i-na-i harmonic 58.320 124.200 # SOURCE3 1 + angle_coeff @angle:i-na-nc harmonic 56.940 120.030 # SOURCE3 4 2.0032 + angle_coeff @angle:i-na-nd harmonic 56.940 120.030 # SOURCE3 4 same_as_i-na-nc + angle_coeff @angle:i-na-os harmonic 59.850 109.910 # SOURCE3 1 0.0000 + angle_coeff @angle:i-na-p2 harmonic 57.960 122.280 # SOURCE3 1 + angle_coeff @angle:i-na-pc harmonic 58.320 121.400 # SOURCE3 3 2.4763 + angle_coeff @angle:i-na-pd harmonic 58.320 121.400 # SOURCE3 3 same_as_i-na-pc + angle_coeff @angle:i-na-ss harmonic 74.730 118.400 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-na-n2 harmonic 70.350 116.710 # SOURCE3 1 + angle_coeff @angle:n2-na-nc harmonic 69.850 119.960 # SOURCE3 4 4.5041 + angle_coeff @angle:n2-na-nd harmonic 69.850 119.960 # SOURCE3 4 same_as_n2-na-nc + angle_coeff @angle:n2-na-os harmonic 70.330 111.530 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-na-p2 harmonic 61.200 124.880 # SOURCE3 1 + angle_coeff @angle:n2-na-pc harmonic 62.110 123.180 # SOURCE3 3 4.7947 + angle_coeff @angle:n2-na-pd harmonic 62.110 123.180 # SOURCE3 3 same_as_n2-na-pc + angle_coeff @angle:n2-na-ss harmonic 78.110 124.640 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-na-n3 harmonic 65.770 124.000 # SOURCE3 1 + angle_coeff @angle:n4-na-n4 harmonic 68.570 111.700 # SOURCE3 1 + angle_coeff @angle:n4-na-nc harmonic 69.090 116.440 # SOURCE3 4 3.6604 + angle_coeff @angle:n4-na-nd harmonic 69.090 116.440 # SOURCE3 4 same_as_n4-na-nc + angle_coeff @angle:n4-na-os harmonic 71.610 102.970 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-na-p2 harmonic 60.870 123.560 # SOURCE3 1 + angle_coeff @angle:n4-na-pc harmonic 61.710 121.980 # SOURCE3 3 4.4884 + angle_coeff @angle:n4-na-pd harmonic 61.710 121.980 # SOURCE3 3 same_as_n4-na-pc + angle_coeff @angle:na-na-na harmonic 66.770 123.600 # SOURCE3 1 + angle_coeff @angle:na-na-nc harmonic 69.080 119.640 # SOURCE3 4 1.6920 + angle_coeff @angle:na-na-nd harmonic 69.080 119.640 # SOURCE3 4 same_as_na-na-nc + angle_coeff @angle:na-na-os harmonic 70.250 109.470 # SOURCE3 1 0.0000 + angle_coeff @angle:na-na-p2 harmonic 61.690 121.720 # SOURCE3 1 + angle_coeff @angle:na-na-pc harmonic 62.360 120.910 # SOURCE3 3 2.3033 + angle_coeff @angle:na-na-pd harmonic 62.360 120.910 # SOURCE3 3 same_as_na-na-pc + angle_coeff @angle:na-na-ss harmonic 80.370 116.500 # SOURCE3 1 0.0000 + angle_coeff @angle:nc-na-nc harmonic 71.200 117.080 # SOURCE3 31 1.8121 + angle_coeff @angle:nc-na-nd harmonic 69.530 122.770 # SOURCE4 5 0.1352 + angle_coeff @angle:nc-na-nh harmonic 68.820 120.550 # SOURCE3 8 1.1436 + angle_coeff @angle:nc-na-no harmonic 68.190 119.150 # SOURCE3 4 1.6049 + angle_coeff @angle:nc-na-o harmonic 72.040 122.790 # SOURCE3 6 1.3154 + angle_coeff @angle:nc-na-oh harmonic 69.710 119.220 # SOURCE3 4 1.7201 + angle_coeff @angle:nc-na-os harmonic 68.300 119.650 # SOURCE3 4 1.5019 + angle_coeff @angle:nc-na-p2 harmonic 62.600 119.990 # SOURCE3 4 3.6009 + angle_coeff @angle:nc-na-p3 harmonic 62.200 120.070 # SOURCE3 4 3.7188 + angle_coeff @angle:nc-na-p4 harmonic 68.140 119.770 # SOURCE3 3 0.3747 + angle_coeff @angle:nc-na-p5 harmonic 63.880 118.950 # SOURCE3 4 3.1194 + angle_coeff @angle:nc-na-pc harmonic 63.450 118.660 # SOURCE3 27 1.5082 + angle_coeff @angle:nc-na-s4 harmonic 77.870 119.200 # SOURCE3 4 2.3841 + angle_coeff @angle:nc-na-s6 harmonic 80.300 119.240 # SOURCE3 4 2.2262 + angle_coeff @angle:nc-na-s harmonic 77.910 122.260 # SOURCE3 4 0.9173 + angle_coeff @angle:nc-na-sh harmonic 80.100 120.500 # SOURCE3 4 1.5016 + angle_coeff @angle:nc-na-ss harmonic 79.650 120.500 # SOURCE3 4 1.5615 + angle_coeff @angle:nd-na-nd harmonic 71.200 117.080 # SOURCE3 31 1.8121 + angle_coeff @angle:nd-na-nh harmonic 68.820 120.550 # SOURCE3 8 same_as_nc-na-nh + angle_coeff @angle:nd-na-no harmonic 68.190 119.150 # SOURCE3 4 same_as_nc-na-no + angle_coeff @angle:nd-na-o harmonic 72.040 122.790 # SOURCE3 6 same_as_nc-na-o + angle_coeff @angle:nd-na-oh harmonic 69.710 119.220 # SOURCE3 4 same_as_nc-na-oh + angle_coeff @angle:nd-na-os harmonic 68.300 119.650 # SOURCE3 4 same_as_nc-na-os + angle_coeff @angle:nd-na-p2 harmonic 62.600 119.990 # SOURCE3 4 same_as_nc-na-p2 + angle_coeff @angle:nd-na-p3 harmonic 62.200 120.070 # SOURCE3 4 same_as_nc-na-p3 + angle_coeff @angle:nd-na-p4 harmonic 68.140 119.770 # SOURCE3 3 same_as_nc-na-p4 + angle_coeff @angle:nd-na-p5 harmonic 63.880 118.950 # SOURCE3 4 same_as_nc-na-p5 + angle_coeff @angle:nd-na-pd harmonic 63.450 118.660 # SOURCE3 27 same_as_nc-na-pc + angle_coeff @angle:nd-na-s4 harmonic 77.870 119.200 # SOURCE3 4 same_as_nc-na-s4 + angle_coeff @angle:nd-na-s6 harmonic 80.300 119.240 # SOURCE3 4 same_as_nc-na-s6 + angle_coeff @angle:nd-na-s harmonic 77.910 122.260 # SOURCE3 4 same_as_nc-na-s + angle_coeff @angle:nd-na-sh harmonic 80.100 120.500 # SOURCE3 4 same_as_nc-na-sh + angle_coeff @angle:nd-na-ss harmonic 79.650 120.500 # SOURCE3 4 same_as_nc-na-ss + angle_coeff @angle:nh-na-nh harmonic 66.770 123.600 # SOURCE3 1 + angle_coeff @angle:nh-na-os harmonic 69.650 111.370 # SOURCE3 1 0.0000 + angle_coeff @angle:nh-na-p2 harmonic 61.900 120.860 # SOURCE3 1 + angle_coeff @angle:nh-na-pc harmonic 62.500 120.380 # SOURCE3 6 1.3513 + angle_coeff @angle:nh-na-pd harmonic 62.500 120.380 # SOURCE3 6 same_as_nh-na-pc + angle_coeff @angle:nh-na-ss harmonic 81.840 112.350 # SOURCE3 2 5.2951 + angle_coeff @angle:n-na-n harmonic 67.780 123.800 # SOURCE3 1 + angle_coeff @angle:n-na-nc harmonic 69.610 119.850 # SOURCE3 4 1.6156 + angle_coeff @angle:n-na-nd harmonic 69.610 119.850 # SOURCE3 4 same_as_n-na-nc + angle_coeff @angle:no-na-no harmonic 65.220 122.800 # SOURCE3 1 + angle_coeff @angle:no-na-os harmonic 70.300 106.550 # SOURCE3 1 0.0000 + angle_coeff @angle:no-na-pc harmonic 62.140 120.110 # SOURCE3 3 2.0821 + angle_coeff @angle:no-na-pd harmonic 62.140 120.110 # SOURCE3 3 same_as_no-na-pc + angle_coeff @angle:n-na-os harmonic 72.340 104.710 # SOURCE3 1 0.0000 + angle_coeff @angle:no-na-ss harmonic 80.360 114.950 # SOURCE3 1 0.0000 + angle_coeff @angle:n-na-p2 harmonic 61.990 121.350 # SOURCE3 1 + angle_coeff @angle:n-na-pc harmonic 62.650 120.640 # SOURCE3 3 2.0168 + angle_coeff @angle:n-na-pd harmonic 62.650 120.640 # SOURCE3 3 same_as_n-na-pc + angle_coeff @angle:n-na-ss harmonic 80.800 116.100 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-na-oh harmonic 68.130 122.200 # SOURCE3 1 + angle_coeff @angle:oh-na-p2 harmonic 62.330 120.760 # SOURCE3 1 + angle_coeff @angle:oh-na-pc harmonic 63.000 119.990 # SOURCE3 3 2.1734 + angle_coeff @angle:oh-na-pd harmonic 63.000 119.990 # SOURCE3 3 same_as_oh-na-pc + angle_coeff @angle:oh-na-ss harmonic 82.110 113.040 # SOURCE3 1 0.0000 + angle_coeff @angle:o-na-o harmonic 74.030 126.200 # SOURCE3 1 + angle_coeff @angle:o-na-os harmonic 70.760 118.390 # SOURCE3 1 0.0000 + angle_coeff @angle:o-na-p2 harmonic 62.830 122.800 # SOURCE3 1 + angle_coeff @angle:o-na-pc harmonic 63.490 122.340 # SOURCE3 3 1.2908 + angle_coeff @angle:o-na-pd harmonic 63.490 122.340 # SOURCE3 3 same_as_o-na-pc + angle_coeff @angle:os-na-os harmonic 71.290 104.450 # SOURCE3 2 0.0983 + angle_coeff @angle:os-na-p2 harmonic 62.590 117.860 # SOURCE3 1 0.0000 + angle_coeff @angle:os-na-p3 harmonic 66.040 104.700 # SOURCE3 1 0.0000 + angle_coeff @angle:os-na-p5 harmonic 65.290 111.410 # SOURCE3 1 0.0000 + angle_coeff @angle:os-na-pc harmonic 62.490 119.910 # SOURCE3 3 1.9002 + angle_coeff @angle:os-na-pd harmonic 62.490 119.910 # SOURCE3 3 same_as_os-na-pc + angle_coeff @angle:os-na-s4 harmonic 82.020 105.880 # SOURCE3 2 0.0000 + angle_coeff @angle:os-na-s6 harmonic 82.010 112.000 # SOURCE3 2 0.0000 + angle_coeff @angle:os-na-ss harmonic 82.680 109.640 # SOURCE3 3 4.1395 + angle_coeff @angle:p2-na-p2 harmonic 60.320 120.910 # SOURCE3 1 + angle_coeff @angle:p2-na-p3 harmonic 59.150 124.800 # SOURCE3 1 + angle_coeff @angle:p2-na-p5 harmonic 60.140 123.990 # SOURCE3 1 + angle_coeff @angle:p2-na-pc harmonic 60.660 120.720 # SOURCE3 3 0.2407 + angle_coeff @angle:p2-na-pd harmonic 60.660 120.720 # SOURCE3 3 same_as_p2-na-pc + angle_coeff @angle:p2-na-s4 harmonic 74.880 122.470 # SOURCE3 1 + angle_coeff @angle:p2-na-s6 harmonic 76.310 122.500 # SOURCE3 1 + angle_coeff @angle:p2-na-s harmonic 75.690 121.850 # SOURCE3 1 + angle_coeff @angle:p2-na-sh harmonic 76.680 121.750 # SOURCE3 1 + angle_coeff @angle:p2-na-ss harmonic 76.380 121.880 # SOURCE3 1 + angle_coeff @angle:p3-na-p3 harmonic 58.510 126.600 # SOURCE3 1 + angle_coeff @angle:p3-na-pc harmonic 59.780 123.320 # SOURCE3 3 4.1781 + angle_coeff @angle:p3-na-pd harmonic 59.780 123.320 # SOURCE3 3 same_as_p3-na-pc + angle_coeff @angle:p5-na-p5 harmonic 60.590 124.600 # SOURCE3 1 + angle_coeff @angle:p5-na-pc harmonic 60.760 122.690 # SOURCE3 3 3.6738 + angle_coeff @angle:p5-na-pd harmonic 60.760 122.690 # SOURCE3 3 same_as_p5-na-pc + angle_coeff @angle:p5-na-ss harmonic 78.220 118.520 # SOURCE3 1 0.0000 + angle_coeff @angle:pc-na-pc harmonic 60.940 120.780 # SOURCE3 27 1.6457 + angle_coeff @angle:pc-na-s4 harmonic 75.520 121.510 # SOURCE3 3 2.7242 + angle_coeff @angle:pc-na-s6 harmonic 76.990 121.550 # SOURCE3 3 2.7065 + angle_coeff @angle:pc-na-s harmonic 76.170 121.470 # SOURCE3 3 1.0668 + angle_coeff @angle:pc-na-sh harmonic 77.280 121.080 # SOURCE3 3 1.8942 + angle_coeff @angle:pc-na-ss harmonic 76.970 121.200 # SOURCE3 3 1.9295 + angle_coeff @angle:pd-na-pd harmonic 60.940 120.780 # SOURCE3 27 same_as_pc-na-pc + angle_coeff @angle:pd-na-s4 harmonic 75.520 121.510 # SOURCE3 3 same_as_pc-na-s4 + angle_coeff @angle:pd-na-s6 harmonic 76.990 121.550 # SOURCE3 3 same_as_pc-na-s6 + angle_coeff @angle:pd-na-s harmonic 76.170 121.470 # SOURCE3 3 same_as_pc-na-s + angle_coeff @angle:pd-na-sh harmonic 77.280 121.080 # SOURCE3 3 same_as_pc-na-sh + angle_coeff @angle:pd-na-ss harmonic 76.970 121.200 # SOURCE3 3 same_as_pc-na-ss + angle_coeff @angle:py-na-py harmonic 76.600 78.250 # SOURCE3 1 0.0000 + angle_coeff @angle:s4-na-s4 harmonic 92.990 124.200 # SOURCE3 1 + angle_coeff @angle:s4-na-s6 harmonic 99.310 112.860 # SOURCE3 1 + angle_coeff @angle:s4-na-ss harmonic 99.570 111.920 # SOURCE3 1 0.0000 + angle_coeff @angle:s6-na-s6 harmonic 96.930 123.200 # SOURCE3 1 + angle_coeff @angle:s6-na-ss harmonic 98.410 119.100 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-na-sh harmonic 96.720 124.600 # SOURCE3 1 + angle_coeff @angle:sh-na-ss harmonic 98.710 118.790 # SOURCE3 1 0.0000 + angle_coeff @angle:s-na-s harmonic 93.790 126.000 # SOURCE3 1 + angle_coeff @angle:s-na-ss harmonic 100.150 112.490 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-na-ss harmonic 100.760 113.240 # SOURCE3 2 6.6084 + angle_coeff @angle:sy-na-sy harmonic 96.930 123.200 # SOURCE3 1 + angle_coeff @angle:ca-nb-ca harmonic 68.590 115.860 # SOURCE3 46 1.1645 + angle_coeff @angle:ca-nb-cp harmonic 68.010 118.040 # SOURCE4 58 0.7819 + angle_coeff @angle:ca-nb-cq harmonic 68.010 118.040 # SOURCE4 58 same as ca-nb-cp + angle_coeff @angle:ca-nb-nb harmonic 69.370 118.890 # SOURCE3 10 0.6031 + angle_coeff @angle:cp-nb-nb harmonic 68.790 121.110 # SOURCE4 12 0.4315 + angle_coeff @angle:nb-nb-nb harmonic 70.440 121.040 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n-br harmonic 66.590 116.200 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n-c harmonic 61.850 120.770 # SOURCE3 5 2.6390 + angle_coeff @angle:br-n-ca harmonic 62.070 118.190 # SOURCE3 1 + angle_coeff @angle:br-n-cc harmonic 62.340 118.190 # SOURCE3 1 same_as_br-n-cd + angle_coeff @angle:br-n-cd harmonic 62.340 118.190 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-n-c1 harmonic 73.520 102.690 # SOURCE3 1 + angle_coeff @angle:c1-n-ca harmonic 65.900 118.880 # SOURCE3 1 + angle_coeff @angle:c1-n-cc harmonic 67.020 118.880 # SOURCE3 1 same_as_c1-n-cd + angle_coeff @angle:c1-n-cd harmonic 67.020 118.880 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-n-c2 harmonic 65.180 116.750 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-n-c3 harmonic 63.060 119.980 # SOURCE4 23 2.3373 + angle_coeff @angle:c2-n-ca harmonic 64.880 116.540 # SOURCE3 1 + angle_coeff @angle:c2-n-cc harmonic 65.850 116.540 # SOURCE3 1 same_as_c2-n-cd + angle_coeff @angle:c2-n-cd harmonic 65.850 116.540 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-n-hn harmonic 47.330 118.360 # SOURCE4 40 1.8005 + angle_coeff @angle:c3-n-c3 harmonic 63.130 115.560 # SOURCE4 392 2.0191 + angle_coeff @angle:c3-n-ca harmonic 62.760 119.960 # SOURCE4 165 2.0808 + angle_coeff @angle:c3-n-cc harmonic 63.380 120.810 # SOURCE4 172 1.6565 + angle_coeff @angle:c3-n-cd harmonic 63.240 121.340 # SOURCE4 95 1.0297 + angle_coeff @angle:c3-n-cy harmonic 62.510 117.110 # SOURCE4 49 1.0344 + angle_coeff @angle:c3-n-hn harmonic 46.040 116.780 # SOURCE3 39 2.1985 + angle_coeff @angle:c3-n-n2 harmonic 64.890 121.680 # SOURCE4 52 1.3175 + angle_coeff @angle:c3-n-n harmonic 66.400 114.820 # SOURCE4 9 0.7008 + angle_coeff @angle:c3-n-nc harmonic 66.990 115.190 # SOURCE4 41 0.8150 + angle_coeff @angle:c3-n-nd harmonic 66.870 115.310 # SOURCE4 7 0.9993 + angle_coeff @angle:c3-n-oh harmonic 66.880 113.050 # SOURCE4 31 0.8144 + angle_coeff @angle:c3-n-os harmonic 66.990 112.650 # SOURCE4 16 1.5399 + angle_coeff @angle:c3-n-sy harmonic 76.610 121.270 # SOURCE4 5 1.1298 + angle_coeff @angle:ca-n-ca harmonic 64.310 117.390 # SOURCE4 39 1.6465 + angle_coeff @angle:ca-n-cc harmonic 64.270 121.000 # SOURCE4 16 1.8986 + angle_coeff @angle:ca-n-cd harmonic 68.060 107.900 # SOURCE4 18 0.3512 + angle_coeff @angle:ca-n-cl harmonic 61.550 117.720 # SOURCE3 1 + angle_coeff @angle:ca-n-f harmonic 64.620 114.920 # SOURCE3 1 + angle_coeff @angle:ca-n-hn harmonic 47.360 115.940 # SOURCE4 537 1.8890 + angle_coeff @angle:ca-n-i harmonic 56.580 119.300 # SOURCE3 1 + angle_coeff @angle:ca-n-n2 harmonic 65.720 122.170 # SOURCE4 5 0.2545 + angle_coeff @angle:ca-n-n4 harmonic 64.150 122.980 # SOURCE3 1 + angle_coeff @angle:ca-n-n harmonic 66.300 118.540 # SOURCE4 21 0.3399 + angle_coeff @angle:ca-n-na harmonic 66.330 119.310 # SOURCE4 16 0.3168 + angle_coeff @angle:ca-n-nc harmonic 68.180 114.630 # SOURCE4 5 0.3030 + angle_coeff @angle:ca-n-nd harmonic 68.570 113.030 # SOURCE3 1 same_as_ca-n-nc + angle_coeff @angle:ca-n-nh harmonic 66.600 116.450 # SOURCE3 1 + angle_coeff @angle:ca-n-p2 harmonic 62.890 112.320 # SOURCE3 1 + angle_coeff @angle:ca-n-p3 harmonic 58.640 125.110 # SOURCE3 1 + angle_coeff @angle:ca-n-s4 harmonic 75.900 118.400 # SOURCE3 1 + angle_coeff @angle:ca-n-s6 harmonic 78.480 117.320 # SOURCE3 1 + angle_coeff @angle:ca-n-ss harmonic 78.660 116.600 # SOURCE3 1 + angle_coeff @angle:c-n-c1 harmonic 68.470 117.040 # SOURCE3 1 0.0000 + angle_coeff @angle:c-n-c2 harmonic 65.090 122.150 # SOURCE3 9 5.1016 + angle_coeff @angle:c-n-c3 harmonic 63.920 121.350 # SOURCE3 54 2.3808 + angle_coeff @angle:c3-nc-cd harmonic 67.600 109.510 # SOURCE3 9 5.4142 + angle_coeff @angle:c-n-c harmonic 65.330 127.140 # SOURCE4 514 2.0111 + angle_coeff @angle:c-n-ca harmonic 64.290 123.710 # SOURCE3 10 3.8159 + angle_coeff @angle:ca-nc-ca harmonic 70.730 109.950 # SOURCE3 1 + angle_coeff @angle:ca-nc-cd harmonic 72.670 104.240 # SOURCE4 187 1.2216 + angle_coeff @angle:ca-nc-n harmonic 73.700 104.690 # SOURCE3 1 + angle_coeff @angle:ca-nc-na harmonic 74.610 102.630 # SOURCE4 13 0.2570 + angle_coeff @angle:ca-nc-os harmonic 73.070 104.500 # SOURCE4 9 0.1740 + angle_coeff @angle:ca-nc-ss harmonic 85.860 116.290 # SOURCE3 1 + angle_coeff @angle:c-n-cc harmonic 65.240 124.190 # SOURCE3 57 2.2262 + angle_coeff @angle:c-nc-ca harmonic 66.430 120.660 # SOURCE3 1 + angle_coeff @angle:cc-n-cc harmonic 68.800 108.920 # SOURCE3 11 0.3167 + angle_coeff @angle:cc-nc-cc harmonic 68.600 110.190 # SOURCE3 1 0.0000 + angle_coeff @angle:cc-nc-cd harmonic 70.480 107.470 # SOURCE3 26 5.4053 + angle_coeff @angle:c-nc-cd harmonic 66.550 120.320 # SOURCE4 76 0.9196 + angle_coeff @angle:cc-n-cl harmonic 62.010 117.720 # SOURCE3 1 same_as_cd-n-cl + angle_coeff @angle:cc-nc-na harmonic 73.380 102.970 # SOURCE3 1 0.0000 + angle_coeff @angle:cc-nc-nd harmonic 72.540 107.940 # SOURCE3 6 1.4052 + angle_coeff @angle:c-n-cd harmonic 65.240 124.190 # SOURCE3 57 2.2262 + angle_coeff @angle:cd-nc-cd harmonic 68.020 119.060 # SOURCE4 7 0.1559 + angle_coeff @angle:cd-nc-n harmonic 69.430 118.060 # SOURCE4 60 1.8266 + angle_coeff @angle:cd-nc-na harmonic 74.240 103.730 # SOURCE3 122 2.3292 + angle_coeff @angle:cd-nc-nc harmonic 72.470 106.430 # SOURCE4 9 0.7064 + angle_coeff @angle:cd-nc-os harmonic 73.170 104.300 # SOURCE4 58 1.0231 + angle_coeff @angle:cd-nc-ss harmonic 88.980 108.340 # SOURCE4 33 1.3882 + angle_coeff @angle:c-n-ce harmonic 62.210 131.830 # SOURCE4 146 1.3048 + angle_coeff @angle:cc-n-f harmonic 65.610 114.920 # SOURCE3 1 same_as_cd-n-f + angle_coeff @angle:cc-n-hn harmonic 48.080 118.710 # SOURCE4 170 2.2963 + angle_coeff @angle:cc-n-i harmonic 56.610 119.300 # SOURCE3 1 same_as_cd-n-i + angle_coeff @angle:c-n-cl harmonic 62.720 116.350 # SOURCE4 11 0.6829 + angle_coeff @angle:cc-n-n2 harmonic 70.090 110.870 # SOURCE3 1 same_as_cd-n-n2 + angle_coeff @angle:cc-n-n harmonic 66.530 121.370 # SOURCE3 1 same_as_cd-n-n + angle_coeff @angle:cc-n-na harmonic 67.870 117.570 # SOURCE3 1 same_as_cd-n-na + angle_coeff @angle:cc-n-nc harmonic 70.120 111.950 # SOURCE4 13 0.6972 + angle_coeff @angle:cc-n-nh harmonic 67.300 117.520 # SOURCE3 1 same_as_cd-n-nh + angle_coeff @angle:cc-n-no harmonic 66.400 115.920 # SOURCE3 1 same_as_cd-n-no + angle_coeff @angle:cc-n-o harmonic 70.070 120.540 # SOURCE3 1 same_as_cd-n-o + angle_coeff @angle:cc-n-oh harmonic 67.320 118.150 # SOURCE3 1 same_as_cd-n-oh + angle_coeff @angle:cc-n-os harmonic 68.060 115.560 # SOURCE3 1 same_as_cd-n-os + angle_coeff @angle:cc-n-p2 harmonic 63.340 112.320 # SOURCE3 1 same_as_cd-n-p2 + angle_coeff @angle:cc-n-p3 harmonic 59.020 125.110 # SOURCE3 1 same_as_cd-n-p3 + angle_coeff @angle:cc-n-p5 harmonic 61.710 121.000 # SOURCE3 1 same_as_cd-n-p5 + angle_coeff @angle:cc-n-s4 harmonic 76.360 118.400 # SOURCE3 1 same_as_cd-n-s4 + angle_coeff @angle:cc-n-s6 harmonic 79.070 117.320 # SOURCE3 1 same_as_cd-n-s6 + angle_coeff @angle:cc-n-s harmonic 76.920 118.290 # SOURCE3 1 same_as_cd-n-s + angle_coeff @angle:cc-n-sh harmonic 78.020 119.130 # SOURCE3 1 same_as_cd-n-sh + angle_coeff @angle:cc-n-ss harmonic 79.250 116.600 # SOURCE3 2 same_as_cd-n-ss + angle_coeff @angle:c-n-cx harmonic 64.220 122.070 # SOURCE4 11 1.9478 + angle_coeff @angle:c-n-cy harmonic 72.260 94.230 # SOURCE4 270 1.3777 + angle_coeff @angle:cd-n-cd harmonic 68.800 108.920 # SOURCE3 11 same_as_cc-n-cc + angle_coeff @angle:cd-n-cl harmonic 62.010 117.720 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-f harmonic 65.610 114.920 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-hn harmonic 47.860 119.820 # SOURCE4 106 1.1020 + angle_coeff @angle:cd-n-i harmonic 56.610 119.300 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-n2 harmonic 70.090 110.870 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-n harmonic 66.530 121.370 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-na harmonic 67.870 117.570 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-nd harmonic 69.680 113.030 # SOURCE3 1 same_as_cc-n-nc + angle_coeff @angle:cd-n-nh harmonic 67.300 117.520 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-no harmonic 66.400 115.920 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-o harmonic 70.070 120.540 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-oh harmonic 67.320 118.150 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-os harmonic 68.060 115.560 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-p2 harmonic 63.340 112.320 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-p3 harmonic 59.020 125.110 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-p5 harmonic 61.710 121.000 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-s4 harmonic 76.360 118.400 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-s6 harmonic 79.070 117.320 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-s harmonic 76.920 118.290 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-sh harmonic 78.020 119.130 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-ss harmonic 79.250 116.600 # SOURCE3 2 1.8318 + angle_coeff @angle:ce-n-cy harmonic 64.680 111.970 # SOURCE4 142 2.1245 + angle_coeff @angle:c-n-f harmonic 68.300 108.630 # SOURCE3 3 4.6785 + angle_coeff @angle:cf-n-cy harmonic 64.910 110.790 # SOURCE4 10 1.1677 + angle_coeff @angle:c-n-hn harmonic 49.210 118.460 # SOURCE3 157 2.4094 + angle_coeff @angle:c-n-i harmonic 56.340 120.380 # SOURCE3 5 2.1600 + angle_coeff @angle:cl-n-cl harmonic 63.240 111.690 # SOURCE3 1 0.0000 + angle_coeff @angle:c-n-n2 harmonic 68.060 120.590 # SOURCE3 9 3.2410 + angle_coeff @angle:c-n-n3 harmonic 67.130 120.430 # SOURCE3 5 0.9481 + angle_coeff @angle:c-n-n4 harmonic 68.850 112.320 # SOURCE3 5 1.2622 + angle_coeff @angle:c-n-n harmonic 68.180 118.420 # SOURCE3 10 2.8922 + angle_coeff @angle:c-n-na harmonic 68.250 119.200 # SOURCE3 11 2.3032 + angle_coeff @angle:na-nc-nd harmonic 75.970 105.470 # SOURCE3 6 0.6349 + angle_coeff @angle:c-n-nc harmonic 67.170 125.230 # SOURCE4 72 2.1204 + angle_coeff @angle:nc-nc-nd harmonic 73.150 111.150 # SOURCE3 3 same_as_nc-nd-nd + angle_coeff @angle:c-n-nd harmonic 67.140 124.930 # SOURCE4 12 2.2148 + angle_coeff @angle:nd-nc-os harmonic 74.420 107.220 # SOURCE3 3 0.4707 + angle_coeff @angle:c-n-nh harmonic 68.020 117.810 # SOURCE4 21 1.5935 + angle_coeff @angle:c-n-no harmonic 66.470 118.160 # SOURCE3 4 5.4870 + angle_coeff @angle:c-n-o harmonic 71.640 118.900 # SOURCE3 9 5.4085 + angle_coeff @angle:c-n-oh harmonic 69.530 113.390 # SOURCE3 6 1.3345 + angle_coeff @angle:c-n-os harmonic 69.600 113.140 # SOURCE3 7 3.0839 + angle_coeff @angle:c-n-p2 harmonic 60.460 124.560 # SOURCE3 8 3.6907 + angle_coeff @angle:c-n-p3 harmonic 59.910 122.540 # SOURCE3 9 4.4802 + angle_coeff @angle:c-n-p4 harmonic 60.710 123.440 # SOURCE3 1 0.0000 + angle_coeff @angle:c-n-p5 harmonic 60.230 128.500 # SOURCE4 6 0.5353 + angle_coeff @angle:c-n-pc harmonic 60.840 122.230 # SOURCE3 3 2.8787 + angle_coeff @angle:c-n-pd harmonic 60.840 122.230 # SOURCE3 3 same_as_c-n-pc + angle_coeff @angle:c-n-s4 harmonic 76.060 120.410 # SOURCE3 4 3.1760 + angle_coeff @angle:c-n-s6 harmonic 77.030 125.010 # SOURCE4 13 1.6314 + angle_coeff @angle:c-n-s harmonic 74.720 126.550 # SOURCE3 3 4.3365 + angle_coeff @angle:c-n-sh harmonic 78.300 119.540 # SOURCE3 4 1.7681 + angle_coeff @angle:c-n-ss harmonic 78.430 120.370 # SOURCE3 7 1.4450 + angle_coeff @angle:c-n-sy harmonic 77.090 124.810 # SOURCE4 51 1.0517 + angle_coeff @angle:cx-n-hn harmonic 46.260 118.580 # SOURCE4 5 0.3288 + angle_coeff @angle:cx-n-os harmonic 97.400 54.040 # SOURCE3 1 0.0000 + angle_coeff @angle:cy-n-hn harmonic 45.340 119.000 # SOURCE4 65 1.3840 + angle_coeff @angle:c3-nd-cc harmonic 67.600 109.510 # SOURCE3 9 same_as_c3-nc-cd + angle_coeff @angle:ca-nd-ca harmonic 70.730 109.950 # SOURCE3 1 same_as_ca-nc-ca + angle_coeff @angle:ca-nd-cc harmonic 72.240 105.470 # SOURCE4 250 2.4919 + angle_coeff @angle:ca-nd-n harmonic 73.580 104.690 # SOURCE3 1 same_as_ca-nc-n + angle_coeff @angle:ca-nd-na harmonic 74.060 104.160 # SOURCE3 1 same_as_ca-nc-na + angle_coeff @angle:ca-nd-nc harmonic 73.550 108.410 # SOURCE4 9 0.1575 + angle_coeff @angle:ca-nd-os harmonic 73.130 104.340 # SOURCE3 1 same_as_ca-nc-os + angle_coeff @angle:ca-nd-ss harmonic 85.860 116.290 # SOURCE3 1 same_as_ca-nc-ss + angle_coeff @angle:c-nd-ca harmonic 65.700 120.660 # SOURCE3 1 same_as_c-nc-ca + angle_coeff @angle:c-nd-cc harmonic 65.710 120.680 # SOURCE4 62 1.4340 + angle_coeff @angle:cc-nd-cc harmonic 68.900 116.040 # SOURCE4 10 0.2861 + angle_coeff @angle:cc-nd-cd harmonic 71.090 105.630 # SOURCE4 1214 2.1301 + angle_coeff @angle:cc-nd-n harmonic 73.800 104.150 # SOURCE3 4 same_as_cd-nc-n + angle_coeff @angle:cc-nd-na harmonic 74.240 103.730 # SOURCE3 122 2.3292 + angle_coeff @angle:cc-nd-nd harmonic 71.970 107.920 # SOURCE4 346 1.6831 + angle_coeff @angle:cc-nd-os harmonic 72.920 105.010 # SOURCE4 58 0.4186 + angle_coeff @angle:cc-nd-ss harmonic 89.270 107.640 # SOURCE4 12 0.4724 + angle_coeff @angle:cd-nd-cd harmonic 70.890 103.170 # SOURCE4 5 0.0317 + angle_coeff @angle:cd-nd-na harmonic 73.380 102.970 # SOURCE3 1 same_as_cc-nc-na + angle_coeff @angle:cd-nd-nc harmonic 72.540 107.940 # SOURCE3 6 1.4052 + angle_coeff @angle:na-nd-nc harmonic 75.970 105.470 # SOURCE3 6 0.6349 + angle_coeff @angle:nc-nd-nd harmonic 73.100 111.300 # SOURCE4 58 0.2082 + angle_coeff @angle:nc-nd-os harmonic 74.420 107.220 # SOURCE3 3 same_as_nd-nc-os + angle_coeff @angle:c1-ne-ca harmonic 60.080 152.480 # SOURCE4 8 1.5840 + angle_coeff @angle:c1-ne-cg harmonic 66.000 140.000 # SOURCE2 1 0.0000 + angle_coeff @angle:c2-ne-ca harmonic 66.060 120.920 # SOURCE4 53 1.9651 + angle_coeff @angle:c2-ne-ce harmonic 67.330 118.170 # SOURCE3 3 1.2374 + angle_coeff @angle:c2-ne-cg harmonic 68.360 123.580 # SOURCE4 12 0.8560 + angle_coeff @angle:c2-ne-n2 harmonic 74.560 113.310 # SOURCE3 1 + angle_coeff @angle:c2-ne-ne harmonic 69.170 110.860 # SOURCE3 7 4.5874 + angle_coeff @angle:c2-ne-p2 harmonic 63.870 134.030 # SOURCE3 1 + angle_coeff @angle:c2-ne-pe harmonic 62.610 120.520 # SOURCE3 8 8.1381 + angle_coeff @angle:c2-ne-px harmonic 63.660 117.750 # SOURCE3 5 0.8581 + angle_coeff @angle:c2-ne-py harmonic 66.630 117.040 # SOURCE3 3 1.4398 + angle_coeff @angle:c2-ne-sx harmonic 77.140 111.980 # SOURCE3 3 0.4090 + angle_coeff @angle:c2-ne-sy harmonic 77.530 120.970 # SOURCE4 6 0.2394 + angle_coeff @angle:ca-ne-cf harmonic 65.630 121.760 # SOURCE4 9 1.9872 + angle_coeff @angle:ca-ne-n2 harmonic 69.660 114.270 # SOURCE4 9 0.4600 + angle_coeff @angle:ca-ne-nf harmonic 69.710 115.050 # SOURCE4 22 0.7409 + angle_coeff @angle:ca-ne-o harmonic 71.100 113.960 # SOURCE3 3 1.1253 + angle_coeff @angle:ca-ne-p2 harmonic 65.650 118.090 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-ne-s harmonic 83.220 120.110 # SOURCE3 1 0.0000 + angle_coeff @angle:c-ne-c2 harmonic 67.860 118.530 # SOURCE3 3 3.2058 + angle_coeff @angle:ce-ne-n2 harmonic 71.160 111.190 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-ne-o harmonic 72.260 112.160 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-ne-p2 harmonic 66.250 117.020 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-ne-s harmonic 84.980 116.280 # SOURCE3 1 0.0000 + angle_coeff @angle:cg-ne-n1 harmonic 71.710 120.200 # SOURCE2 1 0.0000 + angle_coeff @angle:cg-ne-n2 harmonic 73.160 113.390 # SOURCE3 1 0.0000 + angle_coeff @angle:cg-ne-o harmonic 74.430 114.700 # SOURCE2 1 0.0000 + angle_coeff @angle:cg-ne-p2 harmonic 66.960 119.570 # SOURCE3 1 0.0000 + angle_coeff @angle:cg-ne-s harmonic 86.420 117.700 # SOURCE3 1 0.0000 + angle_coeff @angle:c-ne-sy harmonic 78.040 116.050 # SOURCE4 6 1.2661 + angle_coeff @angle:n2-ne-n2 harmonic 78.590 107.220 # SOURCE3 1 + angle_coeff @angle:n2-ne-ne harmonic 70.940 110.720 # SOURCE3 9 6.1488 + angle_coeff @angle:n2-ne-o harmonic 78.090 114.100 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-ne-p2 harmonic 72.370 109.660 # SOURCE3 1 + angle_coeff @angle:n2-ne-pe harmonic 66.510 112.150 # SOURCE3 7 6.5273 + angle_coeff @angle:n2-ne-px harmonic 65.740 115.970 # SOURCE3 3 1.9854 + angle_coeff @angle:n2-ne-py harmonic 69.010 114.600 # SOURCE3 3 2.9261 + angle_coeff @angle:n2-ne-s harmonic 90.200 115.900 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-ne-sx harmonic 80.750 107.290 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-ne-sy harmonic 82.850 111.210 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-ne-o harmonic 72.280 110.450 # SOURCE3 10 1.8535 + angle_coeff @angle:ne-ne-p2 harmonic 67.420 114.390 # SOURCE3 6 4.0528 + angle_coeff @angle:ne-ne-s harmonic 85.550 115.950 # SOURCE3 6 3.4604 + angle_coeff @angle:o-ne-o harmonic 76.910 124.090 # SOURCE3 2 8.7534 + angle_coeff @angle:o-ne-pe harmonic 61.880 132.320 # SOURCE3 11 23.9559 + angle_coeff @angle:o-ne-px harmonic 68.040 110.620 # SOURCE3 1 0.0000 + angle_coeff @angle:o-ne-py harmonic 71.120 110.790 # SOURCE3 4 1.6818 + angle_coeff @angle:o-ne-s harmonic 91.120 117.190 # SOURCE3 2 0.0225 + angle_coeff @angle:o-ne-sx harmonic 80.740 108.920 # SOURCE3 1 0.0000 + angle_coeff @angle:o-ne-sy harmonic 83.600 111.340 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-ne-pe harmonic 65.270 116.810 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-ne-px harmonic 62.490 128.350 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-ne-py harmonic 65.650 123.470 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-ne-sx harmonic 80.480 112.120 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-ne-sy harmonic 81.800 115.730 # SOURCE3 1 0.0000 + angle_coeff @angle:pe-ne-s harmonic 83.520 115.730 # SOURCE3 1 0.0000 + angle_coeff @angle:px-ne-s harmonic 78.540 131.840 # SOURCE3 1 0.0000 + angle_coeff @angle:py-ne-s harmonic 86.300 116.180 # SOURCE3 4 3.7135 + angle_coeff @angle:s-ne-s harmonic 109.960 120.870 # SOURCE3 1 0.0000 + angle_coeff @angle:s-ne-sx harmonic 101.960 112.960 # SOURCE3 1 0.0000 + angle_coeff @angle:s-ne-sy harmonic 102.420 119.630 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-nf-ca harmonic 63.220 137.740 # SOURCE3 1 same_as_c1-ne-ca + angle_coeff @angle:c1-nf-ch harmonic 66.000 140.000 # SOURCE2 1 same_as_c1-ne-cg + angle_coeff @angle:c2-nf-ca harmonic 66.690 118.670 # SOURCE3 2 same_as_c2-ne-ca + angle_coeff @angle:c2-nf-cf harmonic 67.330 118.170 # SOURCE3 3 same_as_c2-ne-ce + angle_coeff @angle:c2-nf-n2 harmonic 74.560 113.310 # SOURCE3 1 same_as_c2-ne-n2 + angle_coeff @angle:c2-nf-nf harmonic 69.170 110.860 # SOURCE3 7 same_as_c2-ne-ne + angle_coeff @angle:c2-nf-p2 harmonic 63.870 134.030 # SOURCE3 1 same_as_c2-ne-p2 + angle_coeff @angle:c2-nf-pf harmonic 62.610 120.520 # SOURCE3 8 same_as_c2-ne-pe + angle_coeff @angle:c2-nf-px harmonic 63.660 117.750 # SOURCE3 5 same_as_c2-ne-px + angle_coeff @angle:c2-nf-py harmonic 66.630 117.040 # SOURCE3 3 same_as_c2-ne-py + angle_coeff @angle:c2-nf-sx harmonic 77.140 111.980 # SOURCE3 3 same_as_c2-ne-sx + angle_coeff @angle:c2-nf-sy harmonic 79.580 114.810 # SOURCE3 3 same_as_c2-ne-sy + angle_coeff @angle:ca-nf-ce harmonic 65.450 122.300 # SOURCE4 6 1.8938 + angle_coeff @angle:ca-nf-n2 harmonic 70.020 113.110 # SOURCE3 2 same_as_ca-ne-n2 + angle_coeff @angle:ca-nf-ne harmonic 69.660 115.190 # SOURCE4 22 0.6536 + angle_coeff @angle:ca-nf-o harmonic 71.100 113.960 # SOURCE3 3 same_as_ca-ne-o + angle_coeff @angle:ca-nf-p2 harmonic 65.650 118.090 # SOURCE3 1 same_as_ca-ne-p2 + angle_coeff @angle:ca-nf-s harmonic 83.220 120.110 # SOURCE3 1 same_as_ca-ne-s + angle_coeff @angle:c-nf-c2 harmonic 67.770 118.530 # SOURCE3 3 same_as_c-ne-c2 + angle_coeff @angle:cf-nf-n2 harmonic 71.160 111.190 # SOURCE3 1 same_as_ce-ne-n2 + angle_coeff @angle:cf-nf-o harmonic 72.260 112.160 # SOURCE3 1 same_as_ce-ne-o + angle_coeff @angle:cf-nf-p2 harmonic 66.250 117.020 # SOURCE3 1 same_as_ce-ne-p2 + angle_coeff @angle:cf-nf-s harmonic 84.980 116.280 # SOURCE3 1 same_as_ce-ne-s + angle_coeff @angle:ch-nf-n1 harmonic 71.710 120.200 # SOURCE2 1 same_as_cg-ne-n1 + angle_coeff @angle:ch-nf-n2 harmonic 73.160 113.390 # SOURCE3 1 same_as_cg-ne-n2 + angle_coeff @angle:ch-nf-o harmonic 74.430 114.700 # SOURCE2 1 same_as_cg-ne-o + angle_coeff @angle:ch-nf-p2 harmonic 66.960 119.570 # SOURCE3 1 same_as_cg-ne-p2 + angle_coeff @angle:ch-nf-s harmonic 86.420 117.700 # SOURCE3 1 same_as_cg-ne-s + angle_coeff @angle:f-n-f harmonic 67.900 102.980 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-nf-n2 harmonic 78.590 107.220 # SOURCE3 1 same_as_n2-ne-n2 + angle_coeff @angle:n2-nf-nf harmonic 70.940 110.720 # SOURCE3 9 same_as_n2-ne-ne + angle_coeff @angle:n2-nf-o harmonic 78.090 114.100 # SOURCE3 1 same_as_n2-ne-o + angle_coeff @angle:n2-nf-p2 harmonic 72.370 109.660 # SOURCE3 1 same_as_n2-ne-p2 + angle_coeff @angle:n2-nf-pf harmonic 66.510 112.150 # SOURCE3 7 same_as_n2-ne-pe + angle_coeff @angle:n2-nf-px harmonic 65.740 115.970 # SOURCE3 3 same_as_n2-ne-px + angle_coeff @angle:n2-nf-py harmonic 69.010 114.600 # SOURCE3 3 same_as_n2-ne-py + angle_coeff @angle:n2-nf-s harmonic 90.200 115.900 # SOURCE3 1 same_as_n2-ne-s + angle_coeff @angle:n2-nf-sx harmonic 80.750 107.290 # SOURCE3 1 same_as_n2-ne-sx + angle_coeff @angle:n2-nf-sy harmonic 82.850 111.210 # SOURCE3 1 same_as_n2-ne-sy + angle_coeff @angle:nf-nf-o harmonic 72.280 110.450 # SOURCE3 10 same_as_ne-ne-o + angle_coeff @angle:nf-nf-p2 harmonic 67.420 114.390 # SOURCE3 6 same_as_ne-ne-p2 + angle_coeff @angle:nf-nf-s harmonic 85.550 115.950 # SOURCE3 6 same_as_ne-ne-s + angle_coeff @angle:o-nf-o harmonic 76.910 124.090 # SOURCE3 2 same_as_o-ne-o + angle_coeff @angle:o-nf-pf harmonic 61.880 132.320 # SOURCE3 11 same_as_o-ne-pe + angle_coeff @angle:o-nf-px harmonic 68.040 110.620 # SOURCE3 1 same_as_o-ne-px + angle_coeff @angle:o-nf-py harmonic 71.120 110.790 # SOURCE3 4 same_as_o-ne-py + angle_coeff @angle:o-nf-s harmonic 91.120 117.190 # SOURCE3 2 same_as_o-ne-s + angle_coeff @angle:o-nf-sx harmonic 80.740 108.920 # SOURCE3 1 same_as_o-ne-sx + angle_coeff @angle:o-nf-sy harmonic 83.600 111.340 # SOURCE3 1 same_as_o-ne-sy + angle_coeff @angle:p2-nf-pf harmonic 65.270 116.810 # SOURCE3 1 same_as_p2-ne-pe + angle_coeff @angle:p2-nf-px harmonic 62.490 128.350 # SOURCE3 1 same_as_p2-ne-px + angle_coeff @angle:p2-nf-py harmonic 65.650 123.470 # SOURCE3 1 same_as_p2-ne-py + angle_coeff @angle:p2-nf-sx harmonic 80.480 112.120 # SOURCE3 1 same_as_p2-ne-sx + angle_coeff @angle:p2-nf-sy harmonic 81.800 115.730 # SOURCE3 1 same_as_p2-ne-sy + angle_coeff @angle:pf-nf-s harmonic 83.520 115.730 # SOURCE3 1 same_as_pe-ne-s + angle_coeff @angle:px-nf-s harmonic 78.540 131.840 # SOURCE3 1 same_as_px-ne-s + angle_coeff @angle:py-nf-s harmonic 86.300 116.180 # SOURCE3 4 same_as_py-ne-s + angle_coeff @angle:s-nf-s harmonic 109.960 120.870 # SOURCE3 1 same_as_s-ne-s + angle_coeff @angle:s-nf-sx harmonic 101.960 112.960 # SOURCE3 1 same_as_s-ne-sx + angle_coeff @angle:s-nf-sy harmonic 102.420 119.630 # SOURCE3 1 same_as_s-ne-sy + angle_coeff @angle:br-nh-br harmonic 67.090 106.270 # SOURCE3 1 + angle_coeff @angle:br-nh-ca harmonic 62.040 111.880 # SOURCE3 1 0.0000 + angle_coeff @angle:br-nh-hn harmonic 42.110 101.560 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-nh-c1 harmonic 68.330 116.980 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-nh-c2 harmonic 66.360 122.710 # SOURCE4 5 1.0077 + angle_coeff @angle:c1-nh-ca harmonic 66.220 122.360 # SOURCE3 3 1.2016 + angle_coeff @angle:c1-nh-hn harmonic 49.550 117.300 # SOURCE4 8 0.7120 + angle_coeff @angle:c2-nh-c2 harmonic 65.540 124.500 # SOURCE4 43 1.7515 + angle_coeff @angle:c2-nh-c3 harmonic 63.170 123.710 # SOURCE3 8 3.5348 + angle_coeff @angle:c2-nh-ca harmonic 64.590 127.340 # SOURCE4 97 2.4321 + angle_coeff @angle:c2-nh-cc harmonic 64.990 125.770 # SOURCE4 6 1.4868 + angle_coeff @angle:c2-nh-cd harmonic 64.840 126.330 # SOURCE4 5 0.9167 + angle_coeff @angle:c2-nh-cx harmonic 63.080 124.440 # SOURCE4 10 1.6817 + angle_coeff @angle:c2-nh-hn harmonic 49.620 114.890 # SOURCE4 1000 1.4571 + angle_coeff @angle:c2-nh-n2 harmonic 68.360 120.000 # SOURCE4 33 1.1823 + angle_coeff @angle:c2-nh-n3 harmonic 67.570 116.980 # SOURCE4 14 1.4183 + angle_coeff @angle:c2-nh-no harmonic 66.090 125.630 # SOURCE4 7 0.7554 + angle_coeff @angle:c2-nh-oh harmonic 69.450 112.510 # SOURCE4 12 1.1687 + angle_coeff @angle:c2-nh-os harmonic 69.270 112.930 # SOURCE4 6 0.3945 + angle_coeff @angle:c2-nh-sy harmonic 78.160 121.130 # SOURCE4 10 0.5133 + angle_coeff @angle:c3-nh-c3 harmonic 63.530 114.440 # SOURCE4 523 2.1428 + angle_coeff @angle:c3-nh-ca harmonic 64.560 117.770 # SOURCE3 8 1.7521 + angle_coeff @angle:c3-nh-cc harmonic 63.650 121.180 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-nh-cd harmonic 64.170 119.220 # SOURCE4 162 2.4515 + angle_coeff @angle:c3-nh-cf harmonic 63.620 119.920 # SOURCE4 20 1.8571 + angle_coeff @angle:c3-nh-cz harmonic 63.010 125.510 # SOURCE4 12 0.5177 + angle_coeff @angle:c3-nh-hn harmonic 46.460 114.950 # SOURCE3 19 2.4787 + angle_coeff @angle:c3-nh-n2 harmonic 67.890 112.350 # SOURCE3 9 4.0058 + angle_coeff @angle:c3-nh-n harmonic 67.100 111.710 # SOURCE4 6 2.4251 + angle_coeff @angle:c3-nh-na harmonic 66.920 112.430 # SOURCE4 8 1.4219 + angle_coeff @angle:c3-nh-p2 harmonic 60.930 123.350 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-nh-sy harmonic 78.350 116.120 # SOURCE4 13 1.2830 + angle_coeff @angle:ca-nh-ca harmonic 64.340 127.460 # SOURCE3 2 0.0002 + angle_coeff @angle:ca-nh-cc harmonic 63.730 129.910 # SOURCE4 29 1.3269 + angle_coeff @angle:ca-nh-cd harmonic 63.880 129.310 # SOURCE4 9 1.5610 + angle_coeff @angle:ca-nh-cl harmonic 62.010 113.150 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-nh-cx harmonic 63.110 123.630 # SOURCE4 36 0.5899 + angle_coeff @angle:ca-nh-f harmonic 67.900 106.090 # SOURCE3 3 1.0660 + angle_coeff @angle:ca-nh-hn harmonic 49.080 116.130 # SOURCE4 1780 1.2853 + angle_coeff @angle:ca-nh-i harmonic 55.550 117.830 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-nh-n1 harmonic 69.370 117.130 # HF/6-31G* 1 + angle_coeff @angle:ca-nh-n2 harmonic 67.820 121.110 # SOURCE4 19 0.9700 + angle_coeff @angle:ca-nh-n3 harmonic 68.180 114.210 # SOURCE3 6 2.2412 + angle_coeff @angle:ca-nh-n4 harmonic 68.560 108.940 # SOURCE3 5 0.6562 + angle_coeff @angle:ca-nh-n harmonic 68.070 116.150 # SOURCE4 12 0.8135 + angle_coeff @angle:ca-nh-na harmonic 68.580 114.540 # SOURCE3 8 0.7807 + angle_coeff @angle:ca-nh-nh harmonic 68.490 114.870 # SOURCE3 6 2.1432 + angle_coeff @angle:ca-nh-no harmonic 69.190 113.920 # SOURCE3 4 2.9561 + angle_coeff @angle:ca-nh-o harmonic 69.640 121.920 # SOURCE3 2 3.9630 + angle_coeff @angle:ca-nh-oh harmonic 69.150 112.800 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-nh-os harmonic 69.930 110.170 # SOURCE3 3 0.6448 + angle_coeff @angle:ca-nh-p2 harmonic 61.620 125.270 # SOURCE3 8 5.1798 + angle_coeff @angle:ca-nh-p3 harmonic 60.110 125.700 # SOURCE3 3 5.7796 + angle_coeff @angle:ca-nh-p4 harmonic 61.180 124.010 # SOURCE3 3 2.5810 + angle_coeff @angle:ca-nh-p5 harmonic 61.760 125.610 # SOURCE3 3 0.5287 + angle_coeff @angle:ca-nh-s4 harmonic 78.630 115.620 # SOURCE3 3 0.3434 + angle_coeff @angle:ca-nh-s6 harmonic 77.920 123.530 # SOURCE4 33 2.0385 + angle_coeff @angle:ca-nh-s harmonic 75.150 122.540 # SOURCE3 3 2.7001 + angle_coeff @angle:ca-nh-sh harmonic 78.190 121.410 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-nh-ss harmonic 78.160 121.500 # SOURCE3 3 2.6255 + angle_coeff @angle:ca-nh-sy harmonic 76.750 125.260 # SOURCE4 41 1.7517 + angle_coeff @angle:cc-nh-cx harmonic 63.320 122.820 # SOURCE4 42 1.1841 + angle_coeff @angle:cc-nh-hn harmonic 48.860 117.160 # SOURCE3 11 2.6137 + angle_coeff @angle:cc-nh-n2 harmonic 68.230 119.660 # SOURCE4 5 1.3903 + angle_coeff @angle:cc-nh-sy harmonic 77.480 122.910 # SOURCE4 23 1.2029 + angle_coeff @angle:cd-nh-cx harmonic 62.500 126.090 # SOURCE4 16 2.3269 + angle_coeff @angle:cd-nh-hn harmonic 48.860 117.160 # SOURCE3 11 2.6137 + angle_coeff @angle:ce-nh-hn harmonic 48.340 115.620 # SOURCE4 187 1.0421 + angle_coeff @angle:ce-nh-o harmonic 66.820 129.430 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-nh-sy harmonic 80.450 112.970 # SOURCE4 7 1.0636 + angle_coeff @angle:cf-nh-hn harmonic 48.620 115.620 # SOURCE4 16 1.3549 + angle_coeff @angle:cf-nh-o harmonic 67.070 129.430 # SOURCE3 1 same_as_ce-nh-o + angle_coeff @angle:cl-nh-cl harmonic 62.930 106.600 # SOURCE3 1 + angle_coeff @angle:cl-nh-hn harmonic 43.080 104.140 # SOURCE3 1 0.0000 + angle_coeff @angle:cx-nh-cx harmonic 86.530 62.020 # SOURCE4 45 0.6189 + angle_coeff @angle:cx-nh-hn harmonic 45.790 118.890 # SOURCE4 8 0.1391 + angle_coeff @angle:cz-nh-hn harmonic 48.790 121.240 # SOURCE4 40 0.5682 + angle_coeff @angle:f-nh-f harmonic 66.930 101.700 # SOURCE3 1 0.0000 + angle_coeff @angle:f-nh-hn harmonic 49.800 101.230 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-nh-hn harmonic 40.050 114.850 # SOURCE4 1108 2.0811 + angle_coeff @angle:hn-nh-i harmonic 36.550 107.570 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-nh-n1 harmonic 52.310 110.570 # HF/6-31G* 1 + angle_coeff @angle:hn-nh-n2 harmonic 50.080 118.220 # SOURCE4 75 2.3319 + angle_coeff @angle:hn-nh-n3 harmonic 50.050 109.120 # SOURCE3 5 2.3680 + angle_coeff @angle:hn-nh-n4 harmonic 49.690 104.400 # SOURCE3 3 0.5056 + angle_coeff @angle:hn-nh-n harmonic 50.890 107.960 # SOURCE4 16 1.2025 + angle_coeff @angle:hn-nh-na harmonic 50.950 107.910 # SOURCE3 26 1.5528 + angle_coeff @angle:hn-nh-nh harmonic 50.320 110.640 # SOURCE4 8 1.3390 + angle_coeff @angle:hn-nh-no harmonic 50.990 109.930 # SOURCE4 7 0.2027 + angle_coeff @angle:hn-nh-o harmonic 52.990 116.450 # SOURCE3 2 0.6063 + angle_coeff @angle:hn-nh-oh harmonic 51.130 106.550 # SOURCE4 8 0.4590 + angle_coeff @angle:hn-nh-os harmonic 51.510 104.760 # SOURCE3 3 0.4883 + angle_coeff @angle:hn-nh-p2 harmonic 42.970 118.180 # SOURCE3 21 3.6927 + angle_coeff @angle:hn-nh-p3 harmonic 41.930 116.190 # SOURCE3 3 3.0539 + angle_coeff @angle:hn-nh-p4 harmonic 43.250 112.600 # SOURCE3 3 0.8237 + angle_coeff @angle:hn-nh-p5 harmonic 43.730 115.260 # SOURCE3 3 0.9168 + angle_coeff @angle:hn-nh-s4 harmonic 54.500 107.480 # SOURCE3 3 1.3960 + angle_coeff @angle:hn-nh-s harmonic 51.650 114.370 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-nh-s6 harmonic 55.730 109.980 # SOURCE4 29 0.7478 + angle_coeff @angle:hn-nh-sh harmonic 54.760 112.250 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-nh-ss harmonic 54.360 113.890 # SOURCE3 3 1.4030 + angle_coeff @angle:hn-nh-sy harmonic 54.780 111.230 # SOURCE4 62 1.1413 + angle_coeff @angle:i-nh-i harmonic 59.800 115.820 # SOURCE3 1 + angle_coeff @angle:n1-nh-n1 harmonic 75.130 106.710 # HF/6-31G* 1 + angle_coeff @angle:n2-nh-n2 harmonic 70.760 117.500 # SOURCE3 2 1.1907 + angle_coeff @angle:n2-nh-n3 harmonic 69.630 115.540 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-nh-o harmonic 70.400 126.060 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-nh-n3 harmonic 69.520 110.980 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-nh-n4 harmonic 68.150 108.360 # SOURCE3 1 0.0000 + angle_coeff @angle:na-nh-na harmonic 70.140 112.010 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n-hn harmonic 39.730 117.850 # SOURCE3 15 2.3694 + angle_coeff @angle:nh-nh-nh harmonic 70.070 112.230 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n-i harmonic 36.080 117.240 # SOURCE3 2 0.4435 + angle_coeff @angle:hn-n-n2 harmonic 49.620 118.330 # SOURCE3 5 2.2377 + angle_coeff @angle:hn-n-n3 harmonic 48.690 117.220 # SOURCE4 37 1.3737 + angle_coeff @angle:hn-n-n4 harmonic 48.900 112.680 # SOURCE3 3 1.9746 + angle_coeff @angle:hn-n-n harmonic 50.140 113.120 # SOURCE3 7 3.2954 + angle_coeff @angle:hn-n-na harmonic 50.400 113.550 # SOURCE3 8 1.9324 + angle_coeff @angle:hn-n-nc harmonic 50.760 115.240 # SOURCE4 10 0.4966 + angle_coeff @angle:hn-n-nh harmonic 49.740 113.130 # SOURCE4 12 1.2125 + angle_coeff @angle:hn-n-no harmonic 48.710 110.110 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n-o harmonic 53.830 116.320 # SOURCE3 2 0.0175 + angle_coeff @angle:n-nh-o harmonic 72.070 115.630 # SOURCE3 1 + angle_coeff @angle:hn-n-oh harmonic 50.330 110.710 # SOURCE4 46 1.1278 + angle_coeff @angle:no-nh-no harmonic 72.070 108.550 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n-os harmonic 50.520 109.820 # SOURCE4 12 0.6996 + angle_coeff @angle:hn-n-p2 harmonic 41.490 118.050 # SOURCE3 7 3.0564 + angle_coeff @angle:hn-n-p3 harmonic 40.240 119.630 # SOURCE3 2 0.0000 + angle_coeff @angle:hn-n-p4 harmonic 41.880 115.710 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n-p5 harmonic 43.060 113.200 # SOURCE4 6 1.0341 + angle_coeff @angle:hn-n-s4 harmonic 52.120 112.460 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n-s harmonic 52.060 114.920 # SOURCE3 2 0.0260 + angle_coeff @angle:hn-n-s6 harmonic 54.500 112.180 # SOURCE4 6 0.6101 + angle_coeff @angle:hn-n-sh harmonic 53.400 114.910 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n-ss harmonic 53.620 115.600 # SOURCE3 3 0.6414 + angle_coeff @angle:hn-n-sy harmonic 54.450 112.340 # SOURCE4 38 0.6039 + angle_coeff @angle:oh-nh-oh harmonic 72.150 106.270 # SOURCE3 1 + angle_coeff @angle:o-nh-o harmonic 72.240 128.060 # SOURCE3 1 + angle_coeff @angle:os-nh-os harmonic 72.410 105.270 # SOURCE3 1 + angle_coeff @angle:p2-nh-p2 harmonic 61.230 127.330 # SOURCE3 2 2.7857 + angle_coeff @angle:p3-nh-p3 harmonic 59.950 125.080 # SOURCE3 1 + angle_coeff @angle:p5-nh-p5 harmonic 65.370 112.760 # SOURCE3 1 + angle_coeff @angle:s4-nh-s4 harmonic 100.210 112.390 # SOURCE3 1 + angle_coeff @angle:s6-nh-s6 harmonic 99.870 120.270 # SOURCE3 1 + angle_coeff @angle:sh-nh-sh harmonic 99.730 119.000 # SOURCE3 1 + angle_coeff @angle:s-nh-s harmonic 95.590 118.730 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-nh-ss harmonic 99.620 119.250 # SOURCE3 1 + angle_coeff @angle:i-n-i harmonic 60.660 118.200 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-n-n2 harmonic 70.160 116.890 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-n-n3 harmonic 68.020 117.940 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-n-n4 harmonic 68.420 112.690 # SOURCE3 1 0.0000 + angle_coeff @angle:na-n-na harmonic 69.610 117.380 # SOURCE3 1 0.0000 + angle_coeff @angle:nc-n-nc harmonic 71.080 116.410 # SOURCE3 1 0.0000 + angle_coeff @angle:nc-n-p2 harmonic 63.760 117.210 # SOURCE3 1 + angle_coeff @angle:nc-n-pc harmonic 63.550 117.210 # SOURCE3 1 0.0000 + angle_coeff @angle:nd-n-nd harmonic 70.860 116.410 # SOURCE3 1 same_as_nc-n-nc + angle_coeff @angle:nd-n-p2 harmonic 63.720 117.210 # SOURCE3 1 same_as_nc-n-p2 + angle_coeff @angle:nd-n-pd harmonic 63.510 117.210 # SOURCE3 1 same_as_nc-n-pc + angle_coeff @angle:nh-n-nh harmonic 69.100 115.180 # SOURCE3 1 0.0000 + angle_coeff @angle:n-n-n harmonic 69.890 114.620 # SOURCE3 1 0.0000 + angle_coeff @angle:no-n-no harmonic 68.520 108.660 # SOURCE3 1 0.0000 + angle_coeff @angle:br-no-o harmonic 58.480 113.190 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-no-o harmonic 71.340 116.630 # SOURCE3 6 0.0000 + angle_coeff @angle:c2-no-o harmonic 69.870 116.870 # SOURCE3 8 0.4200 + angle_coeff @angle:c3-no-o harmonic 66.960 116.560 # SOURCE3 6 0.3959 + angle_coeff @angle:ca-no-o harmonic 68.740 118.100 # SOURCE3 10 1.1524 + angle_coeff @angle:cc-no-o harmonic 70.340 117.520 # SOURCE4 198 0.6255 + angle_coeff @angle:cl-no-o harmonic 61.610 115.080 # SOURCE3 2 0.0000 + angle_coeff @angle:c-no-o harmonic 67.100 115.260 # SOURCE3 1 + angle_coeff @angle:hn-no-o harmonic 55.310 115.490 # SOURCE3 2 0.0000 + angle_coeff @angle:oh-n-oh harmonic 72.050 107.260 # SOURCE3 1 0.0000 + angle_coeff @angle:i-no-o harmonic 54.600 116.310 # SOURCE3 2 0.0000 + angle_coeff @angle:n1-no-o harmonic 73.780 115.000 # HF/6-31G* 1 + angle_coeff @angle:n2-no-o harmonic 65.790 115.100 # SOURCE2 2 2.4000 + angle_coeff @angle:n3-no-o harmonic 72.010 115.560 # SOURCE3 6 0.6427 + angle_coeff @angle:n4-no-o harmonic 72.870 109.000 # SOURCE3 2 0.0000 + angle_coeff @angle:na-no-o harmonic 72.240 115.490 # SOURCE3 18 0.5640 + angle_coeff @angle:nh-no-o harmonic 74.080 115.710 # SOURCE3 8 0.4811 + angle_coeff @angle:n-no-o harmonic 71.670 115.410 # SOURCE3 8 0.3748 + angle_coeff @angle:no-no-o harmonic 59.920 112.380 # SOURCE3 4 0.0000 + angle_coeff @angle:o-n-o harmonic 73.390 128.610 # SOURCE3 3 1.0626 + angle_coeff @angle:o-no-o harmonic 77.150 125.130 # SOURCE4 461 0.7605 + angle_coeff @angle:o-no-oh harmonic 74.090 114.700 # SOURCE3 2 0.0000 + angle_coeff @angle:o-no-os harmonic 73.710 114.010 # SOURCE3 8 0.9778 + angle_coeff @angle:o-no-p2 harmonic 64.840 117.380 # SOURCE3 20 0.8083 + angle_coeff @angle:o-no-p3 harmonic 61.420 116.780 # SOURCE3 6 0.4929 + angle_coeff @angle:o-no-p4 harmonic 60.600 116.640 # SOURCE3 6 0.0089 + angle_coeff @angle:o-no-p5 harmonic 61.770 116.690 # SOURCE3 8 0.4507 + angle_coeff @angle:o-no-s4 harmonic 72.320 114.490 # SOURCE3 6 0.5674 + angle_coeff @angle:o-no-s6 harmonic 73.140 114.390 # SOURCE3 6 0.8311 + angle_coeff @angle:o-no-s harmonic 81.060 119.810 # SOURCE3 4 0.0042 + angle_coeff @angle:o-no-sh harmonic 79.650 116.100 # SOURCE3 2 0.0000 + angle_coeff @angle:o-no-ss harmonic 78.810 115.580 # SOURCE3 6 0.5860 + angle_coeff @angle:os-n-os harmonic 72.280 106.530 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-n-p2 harmonic 61.200 119.620 # SOURCE3 1 + angle_coeff @angle:p3-n-p3 harmonic 62.850 108.730 # SOURCE3 3 0.2591 + angle_coeff @angle:p4-n-p4 harmonic 64.210 108.550 # SOURCE3 1 + angle_coeff @angle:p5-n-p5 harmonic 67.920 99.990 # SOURCE3 1 + angle_coeff @angle:pc-n-pc harmonic 60.950 119.620 # SOURCE3 1 0.0000 + angle_coeff @angle:pd-n-pd harmonic 60.950 119.620 # SOURCE3 1 same_as_pc-n-pc + angle_coeff @angle:s4-n-s4 harmonic 97.760 113.750 # SOURCE3 1 0.0000 + angle_coeff @angle:s6-n-s6 harmonic 99.030 119.680 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-n-sh harmonic 98.560 119.030 # SOURCE3 1 0.0000 + angle_coeff @angle:s-n-s harmonic 93.680 126.000 # SOURCE3 1 + angle_coeff @angle:ss-n-ss harmonic 99.420 118.490 # SOURCE3 1 0.0000 + angle_coeff @angle:br-oh-ho harmonic 42.150 101.600 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-oh-ho harmonic 50.200 108.760 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-oh-ho harmonic 49.910 108.980 # SOURCE3 6 2.2379 + angle_coeff @angle:c3-oh-ho harmonic 47.090 108.160 # SOURCE3 42 1.3034 + angle_coeff @angle:ca-oh-ho harmonic 48.850 109.470 # SOURCE3 7 1.0405 + angle_coeff @angle:cc-oh-ho harmonic 50.060 106.970 # SOURCE4 63 1.4230 + angle_coeff @angle:cd-oh-ho harmonic 49.840 107.160 # SOURCE4 54 1.4035 + angle_coeff @angle:ce-oh-ho harmonic 49.700 106.840 # SOURCE4 23 1.5653 + angle_coeff @angle:cf-oh-ho harmonic 50.070 107.190 # SOURCE4 11 0.9954 + angle_coeff @angle:c-oh-ho harmonic 51.190 107.370 # SOURCE3 34 1.6830 + angle_coeff @angle:cl-oh-ho harmonic 43.560 102.400 # SOURCE2 1 0.0000 + angle_coeff @angle:cx-oh-ho harmonic 49.640 106.170 # SOURCE3 3 0.0644 + angle_coeff @angle:cy-oh-ho harmonic 47.620 107.320 # SOURCE4 5 0.4955 + angle_coeff @angle:f-oh-ho harmonic 48.470 96.800 # SOURCE2 1 0.0000 + angle_coeff @angle:ho-oh-ho harmonic 41.930 104.800 # SOURCE2 1 0.0000 + angle_coeff @angle:ho-oh-i harmonic 35.670 107.980 # SOURCE3 2 0.0000 + angle_coeff @angle:ho-oh-n1 harmonic 52.550 107.810 # HF/6-31G* 1 + angle_coeff @angle:ho-oh-n2 harmonic 50.570 102.740 # SOURCE3 9 2.1286 + angle_coeff @angle:ho-oh-n3 harmonic 50.610 102.330 # SOURCE3 5 1.2591 + angle_coeff @angle:ho-oh-n4 harmonic 49.440 106.630 # SOURCE3 3 0.2770 + angle_coeff @angle:ho-oh-n harmonic 50.460 101.030 # SOURCE3 6 1.4086 + angle_coeff @angle:ho-oh-na harmonic 50.240 103.710 # SOURCE3 9 1.2590 + angle_coeff @angle:ho-oh-nh harmonic 49.970 102.420 # SOURCE4 15 0.6819 + angle_coeff @angle:ho-oh-no harmonic 50.310 102.170 # SOURCE3 1 0.0000 + angle_coeff @angle:ho-oh-o harmonic 47.260 100.870 # SOURCE3 1 + angle_coeff @angle:ho-oh-oh harmonic 49.340 98.720 # SOURCE3 2 0.0000 + angle_coeff @angle:ho-oh-os harmonic 49.580 99.690 # SOURCE4 18 0.3384 + angle_coeff @angle:ho-oh-p2 harmonic 44.140 109.450 # SOURCE3 8 3.3491 + angle_coeff @angle:ho-oh-p3 harmonic 42.540 110.640 # SOURCE3 3 0.5191 + angle_coeff @angle:ho-oh-p4 harmonic 43.670 110.190 # SOURCE3 4 0.2372 + angle_coeff @angle:ho-oh-p5 harmonic 44.150 110.140 # SOURCE3 92 3.8033 + angle_coeff @angle:ho-oh-py harmonic 44.390 110.730 # SOURCE3 79 1.7835 + angle_coeff @angle:ho-oh-s4 harmonic 54.130 106.760 # SOURCE4 9 0.4035 + angle_coeff @angle:ho-oh-s harmonic 51.720 100.150 # SOURCE3 2 0.0000 + angle_coeff @angle:ho-oh-s6 harmonic 57.540 109.200 # SOURCE3 13 0.1856 + angle_coeff @angle:ho-oh-sh harmonic 54.390 106.240 # SOURCE3 2 0.0661 + angle_coeff @angle:ho-oh-ss harmonic 54.540 107.060 # SOURCE3 4 0.9967 + angle_coeff @angle:ho-oh-sy harmonic 55.940 106.410 # SOURCE4 33 0.3729 + angle_coeff @angle:br-os-br harmonic 65.080 110.630 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-os-c1 harmonic 66.990 115.020 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-os-c3 harmonic 64.470 113.390 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-os-c2 harmonic 65.950 113.140 # SOURCE3 6 2.1932 + angle_coeff @angle:c2-os-c3 harmonic 64.210 112.090 # SOURCE3 7 4.1809 + angle_coeff @angle:c2-os-ca harmonic 65.430 113.590 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-os-n2 harmonic 64.910 118.130 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-os-na harmonic 68.210 103.850 # SOURCE3 4 0.6297 + angle_coeff @angle:c2-os-os harmonic 68.350 102.770 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-os-p5 harmonic 61.090 126.370 # SOURCE4 7 1.7939 + angle_coeff @angle:c2-os-ss harmonic 79.830 108.130 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-os-c3 harmonic 62.390 112.450 # SOURCE4 1293 1.6468 + angle_coeff @angle:c3-os-ca harmonic 62.270 117.970 # SOURCE4 2495 1.4576 + angle_coeff @angle:c3-os-cc harmonic 62.430 117.580 # SOURCE4 118 1.0660 + angle_coeff @angle:c3-os-cd harmonic 62.560 117.110 # SOURCE4 130 1.0230 + angle_coeff @angle:c3-os-ce harmonic 62.850 115.700 # SOURCE4 31 2.2296 + angle_coeff @angle:c3-os-cf harmonic 62.540 117.850 # SOURCE4 6 1.2514 + angle_coeff @angle:c3-os-cl harmonic 60.430 110.500 # SOURCE2 1 0.0000 + angle_coeff @angle:c3-os-cy harmonic 61.670 115.650 # SOURCE4 5 0.2390 + angle_coeff @angle:c3-os-i harmonic 54.880 113.700 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-os-n1 harmonic 66.310 113.500 # HF/6-31G* 1 + angle_coeff @angle:c3-os-n2 harmonic 65.920 108.120 # SOURCE3 7 0.3048 + angle_coeff @angle:c3-os-n3 harmonic 64.520 110.280 # SOURCE4 14 1.9026 + angle_coeff @angle:c3-os-n4 harmonic 64.880 110.500 # SOURCE3 3 0.5426 + angle_coeff @angle:c3-os-n harmonic 65.400 109.520 # SOURCE4 14 0.6827 + angle_coeff @angle:c3-os-na harmonic 64.540 109.910 # SOURCE3 9 1.8268 + angle_coeff @angle:c3-os-nc harmonic 64.800 112.730 # SOURCE3 2 1.0358 + angle_coeff @angle:c3-os-nd harmonic 64.800 112.730 # SOURCE3 2 same_as_c3-os-nc + angle_coeff @angle:c3-os-nh harmonic 65.220 109.690 # SOURCE4 8 0.1662 + angle_coeff @angle:c3-os-no harmonic 63.890 113.800 # SOURCE4 42 0.2726 + angle_coeff @angle:c3-os-o harmonic 65.620 103.000 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-os-oh harmonic 65.240 107.970 # SOURCE4 11 0.4333 + angle_coeff @angle:c3-os-os harmonic 65.890 105.010 # SOURCE3 7 0.6328 + angle_coeff @angle:c3-os-p2 harmonic 63.400 115.470 # SOURCE3 8 2.6374 + angle_coeff @angle:c3-os-p3 harmonic 60.450 115.970 # SOURCE3 3 0.3597 + angle_coeff @angle:c3-os-p4 harmonic 61.300 117.480 # SOURCE3 4 0.3850 + angle_coeff @angle:c3-os-p5 harmonic 62.000 118.000 # SOURCE3 31 1.2882 + angle_coeff @angle:c3-os-py harmonic 61.690 117.800 # SOURCE3 16 0.9654 + angle_coeff @angle:c3-os-s4 harmonic 77.610 111.500 # SOURCE3 6 1.4240 + angle_coeff @angle:c3-os-s6 harmonic 80.000 115.790 # SOURCE4 60 1.2588 + angle_coeff @angle:c3-os-s harmonic 75.020 109.550 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-os-sh harmonic 78.050 112.820 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-os-ss harmonic 76.870 113.190 # SOURCE3 3 0.2455 + angle_coeff @angle:ca-os-ca harmonic 63.310 119.950 # SOURCE4 107 1.6535 + angle_coeff @angle:ca-os-cc harmonic 67.320 106.320 # SOURCE4 56 2.1614 + angle_coeff @angle:ca-os-cd harmonic 66.250 109.770 # SOURCE3 6 5.0326 + angle_coeff @angle:ca-os-n3 harmonic 65.390 112.190 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-os-na harmonic 66.470 108.240 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-os-nc harmonic 66.090 113.680 # SOURCE3 2 + angle_coeff @angle:ca-os-nd harmonic 66.090 113.680 # SOURCE3 2 + angle_coeff @angle:ca-os-p5 harmonic 61.600 123.420 # SOURCE4 54 1.1358 + angle_coeff @angle:ca-os-s6 harmonic 80.940 116.970 # SOURCE4 15 0.9514 + angle_coeff @angle:c-os-c2 harmonic 64.910 118.020 # SOURCE4 7 0.3666 + angle_coeff @angle:c-os-c3 harmonic 63.630 115.140 # SOURCE3 17 1.8967 + angle_coeff @angle:c-os-c harmonic 64.540 120.640 # SOURCE4 7 1.5114 + angle_coeff @angle:c-os-ca harmonic 63.750 120.870 # SOURCE4 257 1.7209 + angle_coeff @angle:c-os-cc harmonic 64.150 119.620 # SOURCE3 5 6.0675 + angle_coeff @angle:cc-os-cc harmonic 67.250 106.760 # SOURCE4 192 0.6652 + angle_coeff @angle:cc-os-cd harmonic 63.800 118.620 # SOURCE4 14 1.9764 + angle_coeff @angle:c-os-cd harmonic 64.150 119.620 # SOURCE3 5 6.0675 + angle_coeff @angle:cc-os-na harmonic 65.510 111.660 # SOURCE3 28 4.1343 + angle_coeff @angle:cc-os-nc harmonic 68.120 107.230 # SOURCE3 6 2.7507 + angle_coeff @angle:cc-os-os harmonic 66.270 108.470 # SOURCE3 2 0.0000 + angle_coeff @angle:cc-os-ss harmonic 75.750 119.590 # SOURCE3 1 0.0000 + angle_coeff @angle:c-os-cy harmonic 71.750 91.100 # SOURCE3 2 0.0155 + angle_coeff @angle:cd-os-cd harmonic 67.350 106.450 # SOURCE4 60 0.9115 + angle_coeff @angle:cd-os-na harmonic 65.510 111.660 # SOURCE3 28 4.1343 + angle_coeff @angle:cd-os-nd harmonic 68.120 107.230 # SOURCE3 6 2.7507 + angle_coeff @angle:cd-os-os harmonic 66.270 108.470 # SOURCE3 2 same_as_cc-os-os + angle_coeff @angle:cd-os-ss harmonic 75.750 119.590 # SOURCE3 1 same_as_cc-os-ss + angle_coeff @angle:cl-os-cl harmonic 60.450 110.760 # SOURCE3 2 0.0000 + angle_coeff @angle:c-os-n2 harmonic 66.950 112.080 # SOURCE4 6 0.1154 + angle_coeff @angle:c-os-n harmonic 66.830 112.100 # SOURCE4 6 0.6163 + angle_coeff @angle:c-os-oh harmonic 66.500 110.500 # SOURCE3 1 0.0000 + angle_coeff @angle:c-os-os harmonic 66.250 110.280 # SOURCE4 10 1.3612 + angle_coeff @angle:c-os-p5 harmonic 62.330 122.100 # SOURCE4 5 0.5870 + angle_coeff @angle:c-os-sy harmonic 78.280 113.490 # SOURCE3 1 0.0000 + angle_coeff @angle:cx-os-cx harmonic 85.270 61.820 # SOURCE4 107 0.1793 + angle_coeff @angle:cx-os-n harmonic 88.980 59.990 # SOURCE3 1 0.0000 + angle_coeff @angle:cx-os-os harmonic 90.380 56.520 # SOURCE3 2 0.0000 + angle_coeff @angle:cy-os-cy harmonic 68.810 93.400 # SOURCE2 2 1.4000 + angle_coeff @angle:f-os-f harmonic 63.940 103.300 # SOURCE2 1 0.0000 + angle_coeff @angle:f-os-os harmonic 63.940 109.500 # SOURCE2 1 0.0000 + angle_coeff @angle:i-os-i harmonic 58.060 115.670 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-os-n1 harmonic 70.280 117.790 # HF/6-31G* 1 + angle_coeff @angle:n2-os-n2 harmonic 68.760 106.830 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-os-s6 harmonic 84.320 111.300 # SOURCE4 7 0.5651 + angle_coeff @angle:n3-os-n3 harmonic 67.760 104.880 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-os-n4 harmonic 65.660 114.680 # SOURCE3 1 0.0000 + angle_coeff @angle:na-os-na harmonic 66.100 109.590 # SOURCE3 1 0.0000 + angle_coeff @angle:na-os-ss harmonic 81.940 104.340 # SOURCE3 1 0.0000 + angle_coeff @angle:nc-os-nc harmonic 68.170 110.400 # SOURCE2 1 0.0000 + angle_coeff @angle:nc-os-ss harmonic 80.210 110.970 # SOURCE3 1 0.0000 + angle_coeff @angle:nd-os-nd harmonic 68.170 110.400 # SOURCE2 1 same_as_nc-os-nc + angle_coeff @angle:nd-os-ss harmonic 80.210 110.970 # SOURCE3 1 same_as_nc-os-ss + angle_coeff @angle:nh-os-nh harmonic 67.810 108.290 # SOURCE3 1 0.0000 + angle_coeff @angle:n-os-n harmonic 68.080 108.310 # SOURCE3 1 0.0000 + angle_coeff @angle:no-os-no harmonic 66.400 111.860 # SOURCE3 1 0.0000 + angle_coeff @angle:n-os-s6 harmonic 83.370 113.620 # SOURCE4 5 0.0928 + angle_coeff @angle:o-os-o harmonic 62.760 114.680 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-os-p2 harmonic 64.670 120.020 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-os-p5 harmonic 67.590 107.860 # SOURCE3 1 0.0000 + angle_coeff @angle:p3-os-p3 harmonic 60.040 121.220 # SOURCE3 1 0.0000 + angle_coeff @angle:p3-os-py harmonic 65.620 105.580 # SOURCE3 1 0.0000 + angle_coeff @angle:p5-os-p5 harmonic 61.920 126.250 # SOURCE3 1 0.0000 + angle_coeff @angle:s4-os-s4 harmonic 99.450 111.630 # SOURCE3 1 0.0000 + angle_coeff @angle:s6-os-s6 harmonic 103.740 119.070 # SOURCE3 2 0.4318 + angle_coeff @angle:sh-os-sh harmonic 97.950 118.950 # SOURCE3 1 0.0000 + angle_coeff @angle:s-os-s harmonic 91.270 118.080 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-os-ss harmonic 97.420 115.640 # SOURCE3 1 0.0000 + angle_coeff @angle:br-p2-br harmonic 65.020 108.600 # SOURCE3 1 + angle_coeff @angle:br-p2-c2 harmonic 63.020 102.320 # SOURCE3 2 0.0146 + angle_coeff @angle:br-p2-n2 harmonic 64.590 103.330 # SOURCE3 1 0.0000 + angle_coeff @angle:br-p2-o harmonic 63.020 110.870 # SOURCE3 1 0.0000 + angle_coeff @angle:br-p2-p2 harmonic 63.350 115.460 # SOURCE3 4 7.8622 + angle_coeff @angle:br-p2-s harmonic 82.100 110.520 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-p2-c1 harmonic 62.650 99.040 # SOURCE3 1 + angle_coeff @angle:c1-p2-c2 harmonic 63.650 101.290 # SOURCE3 1 + angle_coeff @angle:c1-p2-n2 harmonic 66.100 101.790 # SOURCE3 1 + angle_coeff @angle:c1-p2-o harmonic 66.040 107.620 # SOURCE3 1 + angle_coeff @angle:c1-p2-p2 harmonic 67.310 99.540 # SOURCE3 1 + angle_coeff @angle:c1-p2-s harmonic 82.930 105.900 # SOURCE3 1 + angle_coeff @angle:c2-p2-c2 harmonic 64.650 104.500 # SOURCE3 1 + angle_coeff @angle:c2-p2-c3 harmonic 61.690 101.900 # SOURCE3 4 0.1132 + angle_coeff @angle:c2-p2-ca harmonic 61.990 101.950 # SOURCE3 1 + angle_coeff @angle:c2-p2-cl harmonic 61.200 102.720 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-p2-f harmonic 66.480 103.470 # SOURCE3 2 0.0136 + angle_coeff @angle:c2-p2-hp harmonic 48.160 97.190 # SOURCE3 3 0.0216 + angle_coeff @angle:c2-p2-i harmonic 54.100 101.940 # SOURCE3 2 0.0368 + angle_coeff @angle:c2-p2-n2 harmonic 69.040 99.880 # SOURCE3 1 + angle_coeff @angle:c2-p2-n3 harmonic 67.110 101.800 # SOURCE3 1 + angle_coeff @angle:c2-p2-n4 harmonic 62.450 98.260 # SOURCE3 6 0.1522 + angle_coeff @angle:c2-p2-n harmonic 65.340 103.280 # SOURCE3 4 3.3113 + angle_coeff @angle:c2-p2-na harmonic 64.790 103.990 # SOURCE3 8 1.6834 + angle_coeff @angle:c2-p2-nh harmonic 65.840 105.170 # SOURCE3 8 0.8263 + angle_coeff @angle:c2-p2-no harmonic 66.990 97.970 # SOURCE3 3 0.4175 + angle_coeff @angle:c2-p2-o harmonic 66.350 115.160 # SOURCE3 1 + angle_coeff @angle:c2-p2-oh harmonic 67.930 102.890 # SOURCE3 3 0.8191 + angle_coeff @angle:c2-p2-os harmonic 69.280 102.120 # SOURCE3 4 0.8783 + angle_coeff @angle:c2-p2-p2 harmonic 69.100 99.560 # SOURCE3 1 + angle_coeff @angle:c2-p2-p3 harmonic 60.750 99.270 # SOURCE3 4 1.1590 + angle_coeff @angle:c2-p2-p4 harmonic 60.850 96.940 # SOURCE3 1 + angle_coeff @angle:c2-p2-p5 harmonic 60.620 97.610 # SOURCE3 1 + angle_coeff @angle:c2-p2-s4 harmonic 77.420 95.150 # SOURCE3 1 + angle_coeff @angle:c2-p2-s6 harmonic 77.560 95.510 # SOURCE3 1 + angle_coeff @angle:c2-p2-s harmonic 85.340 105.530 # SOURCE3 1 + angle_coeff @angle:c2-p2-sh harmonic 81.290 101.490 # SOURCE3 3 0.0057 + angle_coeff @angle:c2-p2-ss harmonic 81.300 101.810 # SOURCE3 4 0.5883 + angle_coeff @angle:c3-p2-c3 harmonic 59.710 99.300 # SOURCE3 1 + angle_coeff @angle:c3-p2-n2 harmonic 64.420 100.820 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p2-o harmonic 64.090 106.720 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p2-os harmonic 65.020 101.340 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p2-p2 harmonic 65.390 100.480 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p2-s harmonic 80.980 105.680 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-p2-ca harmonic 60.070 99.700 # SOURCE3 1 + angle_coeff @angle:ca-p2-n2 harmonic 64.770 100.820 # SOURCE3 1 + angle_coeff @angle:ca-p2-n harmonic 66.610 89.970 # SOURCE3 1 + angle_coeff @angle:ca-p2-na harmonic 66.630 89.210 # SOURCE3 1 + angle_coeff @angle:ca-p2-o harmonic 64.430 106.880 # SOURCE3 1 + angle_coeff @angle:ca-p2-s harmonic 80.490 107.930 # SOURCE3 1 + angle_coeff @angle:c-p2-c2 harmonic 62.160 97.300 # SOURCE3 1 + angle_coeff @angle:c-p2-c harmonic 61.190 90.100 # SOURCE3 1 + angle_coeff @angle:ce-p2-o harmonic 64.940 107.440 # SOURCE3 1 + angle_coeff @angle:ce-p2-s harmonic 82.030 105.540 # SOURCE3 1 + angle_coeff @angle:cf-p2-o harmonic 64.940 107.440 # SOURCE3 1 same_as_ce-p2-o + angle_coeff @angle:cf-p2-s harmonic 82.030 105.540 # SOURCE3 1 same_as_ce-p2-s + angle_coeff @angle:cl-p2-cl harmonic 59.120 108.700 # SOURCE3 1 + angle_coeff @angle:cl-p2-n2 harmonic 63.020 103.380 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-p2-o harmonic 61.870 110.570 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-p2-p2 harmonic 64.880 103.110 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-p2-s harmonic 79.650 110.110 # SOURCE3 1 0.0000 + angle_coeff @angle:f-p2-f harmonic 67.450 107.100 # SOURCE3 1 + angle_coeff @angle:f-p2-n2 harmonic 69.660 103.570 # SOURCE3 1 0.0000 + angle_coeff @angle:f-p2-o harmonic 70.010 110.610 # SOURCE3 1 0.0000 + angle_coeff @angle:f-p2-p2 harmonic 68.870 103.480 # SOURCE3 1 0.0000 + angle_coeff @angle:f-p2-s harmonic 83.240 114.710 # SOURCE3 2 5.2794 + angle_coeff @angle:hp-p2-hp harmonic 36.510 98.760 # SOURCE3 1 + angle_coeff @angle:hp-p2-n1 harmonic 49.670 95.180 # SOURCE3 2 1.5708 + angle_coeff @angle:hp-p2-n2 harmonic 51.270 95.540 # SOURCE3 19 4.7352 + angle_coeff @angle:hp-p2-ne harmonic 51.040 100.100 # SOURCE3 14 6.1290 + angle_coeff @angle:hp-p2-nf harmonic 51.040 100.100 # SOURCE3 14 same_as_hp-p2-ne + angle_coeff @angle:hp-p2-o harmonic 51.210 105.580 # SOURCE3 1 0.0000 + angle_coeff @angle:hp-p2-p2 harmonic 48.180 101.880 # SOURCE3 27 12.9535 + angle_coeff @angle:hp-p2-p4 harmonic 41.290 94.510 # SOURCE3 1 0.0000 + angle_coeff @angle:hp-p2-p5 harmonic 42.510 89.070 # SOURCE3 1 0.0000 + angle_coeff @angle:hp-p2-pe harmonic 47.430 97.250 # SOURCE3 16 8.8916 + angle_coeff @angle:hp-p2-pf harmonic 47.430 97.250 # SOURCE3 16 same_as_hp-p2-pe + angle_coeff @angle:hp-p2-s4 harmonic 53.260 89.990 # SOURCE3 1 0.0000 + angle_coeff @angle:hp-p2-s harmonic 61.200 102.520 # SOURCE3 1 0.0000 + angle_coeff @angle:hp-p2-s6 harmonic 54.080 88.130 # SOURCE3 1 0.0000 + angle_coeff @angle:i-p2-i harmonic 57.140 104.160 # SOURCE3 1 + angle_coeff @angle:i-p2-n2 harmonic 55.340 101.770 # SOURCE3 1 0.0000 + angle_coeff @angle:i-p2-o harmonic 53.280 109.510 # SOURCE3 1 0.0000 + angle_coeff @angle:i-p2-p2 harmonic 58.360 102.630 # SOURCE3 1 0.0000 + angle_coeff @angle:i-p2-s harmonic 71.170 110.600 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-p2-n1 harmonic 74.350 86.220 # HF/6-31G* 1 + angle_coeff @angle:n2-p2-n2 harmonic 72.910 98.000 # SOURCE3 1 + angle_coeff @angle:n2-p2-n3 harmonic 70.540 100.420 # SOURCE3 1 + angle_coeff @angle:n2-p2-n4 harmonic 66.370 93.420 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-p2-na harmonic 68.130 102.030 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-p2-nh harmonic 69.830 101.870 # SOURCE3 2 0.8491 + angle_coeff @angle:n2-p2-no harmonic 69.740 98.120 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-p2-o harmonic 69.560 115.340 # SOURCE3 1 + angle_coeff @angle:n2-p2-oh harmonic 68.760 109.720 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-p2-os harmonic 72.480 102.290 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-p2-p3 harmonic 62.580 99.510 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-p2-p4 harmonic 61.230 101.730 # SOURCE3 1 + angle_coeff @angle:n2-p2-p5 harmonic 63.780 93.680 # SOURCE3 1 + angle_coeff @angle:n2-p2-s4 harmonic 78.670 97.830 # SOURCE3 1 + angle_coeff @angle:n2-p2-s6 harmonic 78.860 98.140 # SOURCE3 1 + angle_coeff @angle:n2-p2-s harmonic 85.870 112.940 # SOURCE3 1 + angle_coeff @angle:n2-p2-sh harmonic 84.460 100.820 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-p2-ss harmonic 84.230 101.760 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-p2-n3 harmonic 67.280 106.300 # SOURCE3 1 + angle_coeff @angle:n3-p2-o harmonic 70.570 106.830 # SOURCE3 1 + angle_coeff @angle:n3-p2-p2 harmonic 70.440 100.580 # SOURCE3 1 + angle_coeff @angle:n3-p2-s harmonic 87.340 105.750 # SOURCE3 1 + angle_coeff @angle:n4-p2-n4 harmonic 63.300 88.800 # SOURCE3 1 + angle_coeff @angle:n4-p2-o harmonic 65.000 101.360 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-p2-p2 harmonic 66.570 96.530 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-p2-s harmonic 81.040 104.980 # SOURCE3 1 0.0000 + angle_coeff @angle:na-p2-na harmonic 64.300 106.100 # SOURCE3 1 + angle_coeff @angle:na-p2-o harmonic 68.270 107.460 # SOURCE3 1 0.0000 + angle_coeff @angle:na-p2-s harmonic 84.570 108.150 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-p2-o harmonic 73.070 107.710 # SOURCE3 1 + angle_coeff @angle:ne-p2-s harmonic 89.700 105.500 # SOURCE3 1 + angle_coeff @angle:nf-p2-o harmonic 73.070 107.710 # SOURCE3 1 same_as_ne-p2-o + angle_coeff @angle:nf-p2-s harmonic 89.700 105.500 # SOURCE3 1 same_as_ne-p2-s + angle_coeff @angle:nh-p2-nh harmonic 67.650 104.000 # SOURCE3 1 + angle_coeff @angle:nh-p2-o harmonic 69.920 108.110 # SOURCE3 2 0.6773 + angle_coeff @angle:nh-p2-p2 harmonic 67.910 107.730 # SOURCE3 3 3.1678 + angle_coeff @angle:nh-p2-s harmonic 85.580 109.620 # SOURCE3 2 1.7725 + angle_coeff @angle:n-p2-n2 harmonic 69.610 98.850 # SOURCE3 1 0.0000 + angle_coeff @angle:n-p2-o harmonic 69.470 105.080 # SOURCE3 1 0.0000 + angle_coeff @angle:no-p2-no harmonic 67.260 98.200 # SOURCE3 1 + angle_coeff @angle:no-p2-o harmonic 69.400 104.870 # SOURCE3 1 0.0000 + angle_coeff @angle:no-p2-p2 harmonic 66.610 108.570 # SOURCE3 3 8.2121 + angle_coeff @angle:no-p2-s harmonic 84.470 109.060 # SOURCE3 2 5.4074 + angle_coeff @angle:n-p2-p2 harmonic 68.780 102.120 # SOURCE3 1 0.0000 + angle_coeff @angle:n-p2-s harmonic 83.340 112.340 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-p2-oh harmonic 71.860 100.100 # SOURCE3 1 + angle_coeff @angle:oh-p2-p2 harmonic 69.090 107.820 # SOURCE3 2 2.6708 + angle_coeff @angle:oh-p2-s harmonic 87.090 109.750 # SOURCE3 1 0.0000 + angle_coeff @angle:o-p2-o harmonic 70.950 119.960 # SOURCE3 1 + angle_coeff @angle:o-p2-oh harmonic 70.850 110.460 # SOURCE3 1 0.0000 + angle_coeff @angle:o-p2-os harmonic 72.860 108.810 # SOURCE3 1 0.0000 + angle_coeff @angle:o-p2-p2 harmonic 68.910 114.230 # SOURCE3 1 + angle_coeff @angle:o-p2-p3 harmonic 61.190 106.690 # SOURCE3 1 0.0000 + angle_coeff @angle:o-p2-p4 harmonic 61.150 104.370 # SOURCE3 1 + angle_coeff @angle:o-p2-p5 harmonic 61.090 104.490 # SOURCE3 1 + angle_coeff @angle:o-p2-pe harmonic 59.000 145.960 # SOURCE3 1 + angle_coeff @angle:o-p2-pf harmonic 59.000 145.960 # SOURCE3 1 same_as_o-p2-pe + angle_coeff @angle:o-p2-s4 harmonic 76.220 106.590 # SOURCE3 1 + angle_coeff @angle:o-p2-s6 harmonic 77.110 105.040 # SOURCE3 1 + angle_coeff @angle:o-p2-s harmonic 86.500 117.420 # SOURCE3 1 + angle_coeff @angle:o-p2-sh harmonic 82.540 109.600 # SOURCE3 1 0.0000 + angle_coeff @angle:os-p2-os harmonic 75.140 98.300 # SOURCE3 1 + angle_coeff @angle:os-p2-p2 harmonic 72.150 101.460 # SOURCE3 1 0.0000 + angle_coeff @angle:o-p2-ss harmonic 82.710 109.600 # SOURCE3 1 0.0000 + angle_coeff @angle:os-p2-s harmonic 88.770 108.470 # SOURCE3 3 1.7065 + angle_coeff @angle:p2-p2-n2 harmonic 72.700 97.400 # SOURCE3 1 + angle_coeff @angle:p2-p2-p3 harmonic 63.950 101.730 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-p2-p4 harmonic 63.280 101.980 # SOURCE3 1 + angle_coeff @angle:p2-p2-p5 harmonic 64.100 99.330 # SOURCE3 1 + angle_coeff @angle:p2-p2-s4 harmonic 82.350 95.730 # SOURCE3 1 + angle_coeff @angle:p2-p2-s6 harmonic 82.540 95.950 # SOURCE3 1 + angle_coeff @angle:p2-p2-s harmonic 87.130 111.280 # SOURCE3 1 + angle_coeff @angle:p2-p2-sh harmonic 81.160 113.940 # SOURCE3 3 8.5009 + angle_coeff @angle:p3-p2-p3 harmonic 59.740 101.000 # SOURCE3 1 + angle_coeff @angle:p3-p2-s harmonic 76.850 113.280 # SOURCE3 2 6.7035 + angle_coeff @angle:p4-p2-s harmonic 79.510 103.890 # SOURCE3 1 + angle_coeff @angle:p5-p2-p5 harmonic 62.680 89.400 # SOURCE3 1 + angle_coeff @angle:p5-p2-s harmonic 80.520 101.210 # SOURCE3 1 + angle_coeff @angle:pe-p2-s harmonic 87.030 106.350 # SOURCE3 1 + angle_coeff @angle:pf-p2-s harmonic 87.030 106.350 # SOURCE3 1 same_as_pe-p2-s + angle_coeff @angle:s4-p2-s4 harmonic 102.320 85.300 # SOURCE3 1 + angle_coeff @angle:s6-p2-s6 harmonic 95.800 98.200 # SOURCE3 1 + angle_coeff @angle:sh-p2-sh harmonic 105.800 98.500 # SOURCE3 1 + angle_coeff @angle:s-p2-s harmonic 113.120 106.600 # SOURCE3 1 + angle_coeff @angle:s-p2-s4 harmonic 99.570 105.290 # SOURCE3 1 + angle_coeff @angle:s-p2-s6 harmonic 99.150 106.930 # SOURCE3 1 + angle_coeff @angle:s-p2-sh harmonic 104.500 110.730 # SOURCE3 2 0.0232 + angle_coeff @angle:s-p2-ss harmonic 103.090 114.140 # SOURCE3 4 5.9223 + angle_coeff @angle:ss-p2-ss harmonic 106.390 97.900 # SOURCE3 1 + angle_coeff @angle:br-p3-br harmonic 65.960 103.540 # SOURCE3 1 0.0000 + angle_coeff @angle:br-p3-hp harmonic 43.060 96.360 # SOURCE3 4 0.6701 + angle_coeff @angle:c1-p3-c1 harmonic 61.500 100.500 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-p3-f harmonic 65.100 96.900 # SOURCE2 1 0.0000 + angle_coeff @angle:c1-p3-hp harmonic 44.980 97.670 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-p3-c2 harmonic 59.650 101.770 # SOURCE3 3 0.0000 + angle_coeff @angle:c2-p3-hp harmonic 44.060 97.850 # SOURCE3 4 0.0000 + angle_coeff @angle:c3-p3-c3 harmonic 59.950 99.660 # SOURCE3 40 0.9854 + angle_coeff @angle:c3-p3-ca harmonic 59.600 101.940 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-p3-cl harmonic 61.420 99.890 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p3-f harmonic 63.510 97.800 # SOURCE2 1 0.0000 + angle_coeff @angle:c3-p3-hp harmonic 43.910 97.660 # SOURCE3 9 0.4096 + angle_coeff @angle:c3-p3-n2 harmonic 63.720 96.550 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-p3-n3 harmonic 62.780 101.180 # SOURCE3 10 2.2338 + angle_coeff @angle:c3-p3-n4 harmonic 61.660 96.940 # SOURCE3 6 0.4815 + angle_coeff @angle:c3-p3-n harmonic 61.970 101.770 # SOURCE3 12 2.4449 + angle_coeff @angle:c3-p3-na harmonic 62.590 100.170 # SOURCE3 4 0.0554 + angle_coeff @angle:c3-p3-nh harmonic 61.770 104.500 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-p3-no harmonic 62.270 96.980 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-p3-o harmonic 62.860 111.670 # SOURCE3 28 5.3387 + angle_coeff @angle:c3-p3-oh harmonic 64.890 98.210 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-p3-os harmonic 64.330 99.530 # SOURCE3 3 1.7678 + angle_coeff @angle:c3-p3-p3 harmonic 57.790 100.310 # SOURCE3 18 2.1836 + angle_coeff @angle:c3-p3-p5 harmonic 57.640 100.900 # SOURCE3 10 2.7070 + angle_coeff @angle:c3-p3-s4 harmonic 76.740 98.880 # SOURCE3 8 6.2235 + angle_coeff @angle:c3-p3-s6 harmonic 76.100 101.180 # SOURCE3 12 6.4536 + angle_coeff @angle:c3-p3-sh harmonic 75.720 98.710 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-p3-ss harmonic 75.730 99.370 # SOURCE3 2 0.0000 + angle_coeff @angle:ca-p3-ca harmonic 60.550 99.860 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-p3-hp harmonic 44.340 97.500 # SOURCE3 2 0.0000 + angle_coeff @angle:c-p3-c3 harmonic 60.100 97.060 # SOURCE3 3 1.1490 + angle_coeff @angle:c-p3-c harmonic 58.350 100.900 # SOURCE3 1 0.0000 + angle_coeff @angle:c-p3-hp harmonic 43.390 96.550 # SOURCE3 6 0.5223 + angle_coeff @angle:cl-p3-cl harmonic 62.670 102.820 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-p3-f harmonic 63.640 99.200 # SOURCE2 1 0.0000 + angle_coeff @angle:cl-p3-hp harmonic 44.110 96.300 # SOURCE3 3 0.6203 + angle_coeff @angle:c-p3-os harmonic 70.240 81.320 # SOURCE3 1 0.0000 + angle_coeff @angle:cx-p3-hp harmonic 44.010 95.200 # SOURCE2 1 0.0000 + angle_coeff @angle:f-p3-f harmonic 68.840 97.400 # SOURCE2 8 1.6636 + angle_coeff @angle:f-p3-hp harmonic 48.850 96.410 # SOURCE3 2 0.0000 + angle_coeff @angle:f-p3-n3 harmonic 66.890 100.600 # SOURCE2 1 0.0000 + angle_coeff @angle:f-p3-os harmonic 67.790 102.200 # SOURCE2 1 0.0000 + angle_coeff @angle:f-p3-p3 harmonic 59.520 97.200 # SOURCE2 1 0.0000 + angle_coeff @angle:hp-p3-hp harmonic 35.200 95.520 # SOURCE3 44 2.4200 + angle_coeff @angle:hp-p3-i harmonic 37.430 96.190 # SOURCE3 4 0.6454 + angle_coeff @angle:hp-p3-n1 harmonic 49.970 92.980 # HF/6-31G* 1 + angle_coeff @angle:hp-p3-n2 harmonic 46.470 98.280 # SOURCE3 10 1.8860 + angle_coeff @angle:hp-p3-n3 harmonic 48.110 94.460 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-n4 harmonic 45.300 93.210 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-n harmonic 47.100 95.150 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-na harmonic 46.750 97.270 # SOURCE3 12 0.9318 + angle_coeff @angle:hp-p3-nh harmonic 48.200 94.100 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-no harmonic 46.080 93.060 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-o harmonic 51.150 101.020 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-oh harmonic 49.120 95.950 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-os harmonic 48.580 97.350 # SOURCE3 6 2.8326 + angle_coeff @angle:hp-p3-p2 harmonic 40.920 99.110 # SOURCE3 16 4.3022 + angle_coeff @angle:hp-p3-p3 harmonic 40.500 95.520 # SOURCE3 4 0.0844 + angle_coeff @angle:hp-p3-p4 harmonic 40.370 95.950 # SOURCE3 6 0.0489 + angle_coeff @angle:hp-p3-p5 harmonic 40.510 95.540 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-s4 harmonic 54.390 95.490 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-s6 harmonic 55.380 92.950 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-sh harmonic 53.620 94.210 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-ss harmonic 53.780 94.610 # SOURCE3 2 0.0000 + angle_coeff @angle:i-p3-i harmonic 58.550 105.250 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-p3-n1 harmonic 73.380 90.440 # HF/6-31G* 1 + angle_coeff @angle:n2-p3-n2 harmonic 64.560 103.460 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-p3-n3 harmonic 62.770 113.800 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-p3-o harmonic 68.780 107.100 # SOURCE3 4 0.0000 + angle_coeff @angle:n3-p3-oh harmonic 68.930 98.360 # SOURCE3 1 + angle_coeff @angle:n4-p3-n4 harmonic 61.460 100.530 # SOURCE3 1 0.0000 + angle_coeff @angle:na-p3-na harmonic 63.790 106.220 # SOURCE3 1 + angle_coeff @angle:nh-p3-nh harmonic 64.100 109.110 # SOURCE3 1 0.0000 + angle_coeff @angle:n-p3-n harmonic 64.000 104.580 # SOURCE3 1 + angle_coeff @angle:n-p3-o harmonic 68.400 104.990 # SOURCE3 4 0.0000 + angle_coeff @angle:no-p3-no harmonic 63.350 98.330 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-p3-oh harmonic 68.360 104.480 # SOURCE3 1 0.0000 + angle_coeff @angle:o-p3-o harmonic 69.980 122.180 # SOURCE3 2 7.8556 + angle_coeff @angle:o-p3-p3 harmonic 56.940 116.740 # SOURCE3 14 0.7525 + angle_coeff @angle:o-p3-p5 harmonic 59.320 107.620 # SOURCE3 4 0.0000 + angle_coeff @angle:o-p3-s4 harmonic 78.140 110.700 # SOURCE3 4 0.7259 + angle_coeff @angle:o-p3-s6 harmonic 79.950 106.660 # SOURCE3 6 3.4017 + angle_coeff @angle:os-p3-os harmonic 67.300 106.650 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-p3-p2 harmonic 58.990 103.580 # SOURCE3 1 0.0000 + angle_coeff @angle:p3-p3-p3 harmonic 56.870 105.310 # SOURCE3 4 3.5864 + angle_coeff @angle:p4-p3-p4 harmonic 58.570 99.090 # SOURCE3 1 + angle_coeff @angle:p5-p3-p5 harmonic 58.650 99.100 # SOURCE3 1 0.0000 + angle_coeff @angle:s4-p3-s4 harmonic 100.040 98.260 # SOURCE3 1 0.0000 + angle_coeff @angle:s6-p3-s6 harmonic 100.770 97.780 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-p3-sh harmonic 93.590 107.580 # SOURCE3 1 0.0000 + angle_coeff @angle:s-p3-s harmonic 87.250 131.320 # SOURCE3 1 + angle_coeff @angle:ss-p3-ss harmonic 93.360 109.240 # SOURCE3 1 0.0000 + angle_coeff @angle:br-p4-br harmonic 65.640 110.410 # SOURCE3 1 + angle_coeff @angle:br-p4-o harmonic 60.420 124.800 # SOURCE3 1 + angle_coeff @angle:c2-p4-c2 harmonic 59.340 104.210 # SOURCE3 1 + angle_coeff @angle:c2-p4-hp harmonic 44.230 99.500 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-p4-o harmonic 63.010 113.590 # SOURCE3 1 + angle_coeff @angle:c3-p4-c3 harmonic 59.460 102.550 # SOURCE3 4 0.0192 + angle_coeff @angle:c3-p4-n2 harmonic 62.470 103.170 # SOURCE3 1 + angle_coeff @angle:c3-p4-n3 harmonic 63.130 102.370 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p4-n4 harmonic 60.000 99.570 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p4-n harmonic 62.290 103.260 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p4-na harmonic 60.600 117.670 # SOURCE3 5 19.0404 + angle_coeff @angle:c3-p4-nh harmonic 62.860 102.790 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p4-no harmonic 61.120 99.800 # SOURCE3 3 0.2151 + angle_coeff @angle:c3-p4-o harmonic 61.960 116.440 # SOURCE3 25 2.6494 + angle_coeff @angle:c3-p4-oh harmonic 65.550 98.560 # SOURCE3 2 0.4558 + angle_coeff @angle:c3-p4-os harmonic 65.800 98.010 # SOURCE3 2 0.0931 + angle_coeff @angle:c3-p4-p2 harmonic 56.110 109.270 # SOURCE3 1 + angle_coeff @angle:c3-p4-p3 harmonic 56.940 103.530 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p4-p4 harmonic 60.790 102.120 # SOURCE3 1 + angle_coeff @angle:c3-p4-p5 harmonic 56.380 104.150 # SOURCE3 1 + angle_coeff @angle:c3-p4-sh harmonic 75.720 100.170 # SOURCE3 2 0.0815 + angle_coeff @angle:c3-p4-ss harmonic 75.600 101.190 # SOURCE3 1 + angle_coeff @angle:ca-p4-ca harmonic 58.870 107.770 # SOURCE3 1 + angle_coeff @angle:ca-p4-o harmonic 63.970 111.640 # SOURCE3 1 + angle_coeff @angle:cl-p4-cl harmonic 62.460 103.510 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-p4-o harmonic 61.910 116.530 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p4-hp harmonic 36.070 99.210 # SOURCE3 4 6.4572 + angle_coeff @angle:hp-p4-n1 harmonic 48.330 99.910 # HF/6-31G* 1 + angle_coeff @angle:hp-p4-o harmonic 50.250 109.350 # SOURCE3 6 10.8284 + angle_coeff @angle:hp-p4-p3 harmonic 39.650 98.960 # SOURCE3 4 0.0000 + angle_coeff @angle:hp-p4-s harmonic 49.200 110.240 # SOURCE3 4 4.1081 + angle_coeff @angle:i-p4-i harmonic 61.590 113.220 # SOURCE3 2 6.7916 + angle_coeff @angle:i-p4-o harmonic 60.270 110.220 # SOURCE3 4 9.7726 + angle_coeff @angle:n1-p4-n1 harmonic 68.740 100.610 # HF/6-31G* 1 + angle_coeff @angle:n1-p4-o harmonic 67.970 114.590 # HF/6-31G* 1 + angle_coeff @angle:n2-p4-n2 harmonic 66.360 102.540 # SOURCE3 1 + angle_coeff @angle:n2-p4-o harmonic 65.230 120.280 # SOURCE3 1 + angle_coeff @angle:n3-p4-o harmonic 67.920 113.270 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-p4-o harmonic 63.230 107.610 # SOURCE3 1 0.0000 + angle_coeff @angle:na-p4-o harmonic 72.190 110.600 # SOURCE3 5 1.3133 + angle_coeff @angle:nh-p4-nh harmonic 69.560 95.300 # SOURCE3 1 0.0000 + angle_coeff @angle:nh-p4-o harmonic 66.920 115.860 # SOURCE3 3 3.2712 + angle_coeff @angle:n-p4-o harmonic 65.600 117.990 # SOURCE3 1 0.0000 + angle_coeff @angle:no-p4-o harmonic 63.000 114.690 # SOURCE3 3 0.1070 + angle_coeff @angle:oh-p4-oh harmonic 72.990 95.710 # SOURCE3 1 0.0000 + angle_coeff @angle:o-p4-o harmonic 72.010 117.220 # SOURCE3 6 2.7792 + angle_coeff @angle:o-p4-oh harmonic 68.540 117.390 # SOURCE3 4 1.0083 + angle_coeff @angle:o-p4-os harmonic 68.880 116.670 # SOURCE3 4 0.6923 + angle_coeff @angle:o-p4-p2 harmonic 56.720 121.350 # SOURCE3 1 + angle_coeff @angle:o-p4-p3 harmonic 57.580 114.000 # SOURCE3 3 0.6663 + angle_coeff @angle:o-p4-p4 harmonic 61.640 116.430 # SOURCE3 1 + angle_coeff @angle:o-p4-p5 harmonic 58.150 109.760 # SOURCE3 1 + angle_coeff @angle:o-p4-s4 harmonic 72.350 112.190 # SOURCE3 1 + angle_coeff @angle:o-p4-s6 harmonic 71.250 113.890 # SOURCE3 1 + angle_coeff @angle:o-p4-s harmonic 75.540 112.780 # SOURCE3 2 0.0000 + angle_coeff @angle:o-p4-sh harmonic 74.810 118.090 # SOURCE3 1 + angle_coeff @angle:os-p4-os harmonic 71.510 100.340 # SOURCE3 1 0.0000 + angle_coeff @angle:o-p4-ss harmonic 75.800 116.140 # SOURCE3 4 1.0636 + angle_coeff @angle:p2-p4-p2 harmonic 56.350 110.710 # SOURCE3 1 + angle_coeff @angle:p3-p4-p3 harmonic 54.380 114.980 # SOURCE3 1 0.0000 + angle_coeff @angle:p4-p4-p4 harmonic 61.300 107.380 # SOURCE3 1 + angle_coeff @angle:p5-p4-p5 harmonic 55.630 107.780 # SOURCE3 1 + angle_coeff @angle:s4-p4-s4 harmonic 93.720 96.240 # SOURCE3 1 + angle_coeff @angle:s6-p4-s6 harmonic 90.160 102.360 # SOURCE3 1 + angle_coeff @angle:sh-p4-sh harmonic 98.440 98.810 # SOURCE3 1 0.0000 + angle_coeff @angle:s-p4-s harmonic 93.540 106.300 # SOURCE3 2 25.0119 + angle_coeff @angle:ss-p4-ss harmonic 96.270 104.410 # SOURCE3 1 0.0000 + angle_coeff @angle:br-p5-br harmonic 67.070 103.380 # SOURCE3 1 0.0000 + angle_coeff @angle:br-p5-o harmonic 62.390 114.650 # SOURCE3 3 1.0910 + angle_coeff @angle:br-p5-oh harmonic 65.360 102.920 # SOURCE3 4 0.5468 + angle_coeff @angle:c1-p5-c1 harmonic 62.070 102.890 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-p5-o harmonic 64.450 115.770 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-p5-oh harmonic 66.220 102.790 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-p5-c2 harmonic 57.300 106.560 # SOURCE3 1 + angle_coeff @angle:c2-p5-o harmonic 63.330 109.240 # SOURCE4 7 2.2628 + angle_coeff @angle:c2-p5-oh harmonic 64.000 101.690 # SOURCE3 1 + angle_coeff @angle:c2-p5-os harmonic 63.780 103.340 # SOURCE3 1 + angle_coeff @angle:c3-p5-c3 harmonic 59.060 106.230 # SOURCE3 14 2.6389 + angle_coeff @angle:c3-p5-hp harmonic 43.230 103.620 # SOURCE4 7 1.1616 + angle_coeff @angle:c3-p5-n3 harmonic 63.940 102.760 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p5-o harmonic 63.790 112.500 # SOURCE3 23 4.4203 + angle_coeff @angle:c3-p5-oh harmonic 65.260 101.560 # SOURCE3 17 2.1803 + angle_coeff @angle:c3-p5-os harmonic 65.840 100.770 # SOURCE4 51 2.0928 + angle_coeff @angle:c3-p5-p4 harmonic 55.960 106.270 # SOURCE3 1 + angle_coeff @angle:c3-p5-s harmonic 75.870 113.400 # SOURCE3 4 2.0067 + angle_coeff @angle:c3-p5-ss harmonic 74.660 103.760 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-p5-ca harmonic 59.290 107.530 # SOURCE3 1 + angle_coeff @angle:ca-p5-o harmonic 63.850 113.980 # SOURCE3 1 + angle_coeff @angle:ca-p5-oh harmonic 65.600 101.770 # SOURCE3 1 + angle_coeff @angle:ca-p5-os harmonic 65.310 103.750 # SOURCE3 1 + angle_coeff @angle:c-p5-c harmonic 57.470 104.160 # SOURCE3 1 + angle_coeff @angle:cl-p5-cl harmonic 62.400 103.700 # SOURCE2 1 0.0000 + angle_coeff @angle:cl-p5-o harmonic 62.360 115.320 # SOURCE3 2 0.0000 + angle_coeff @angle:cl-p5-oh harmonic 65.050 102.440 # SOURCE3 2 0.0000 + angle_coeff @angle:c-p5-o harmonic 63.510 107.190 # SOURCE4 16 0.5711 + angle_coeff @angle:c-p5-oh harmonic 63.500 102.120 # SOURCE3 1 + angle_coeff @angle:f-p5-f harmonic 67.910 99.960 # SOURCE2 4 0.9197 + angle_coeff @angle:f-p5-o harmonic 69.070 112.030 # SOURCE4 7 0.5178 + angle_coeff @angle:f-p5-oh harmonic 69.260 101.980 # SOURCE3 2 0.0000 + angle_coeff @angle:f-p5-os harmonic 69.530 102.700 # SOURCE4 5 0.1524 + angle_coeff @angle:f-p5-s harmonic 77.040 117.400 # SOURCE2 1 0.0000 + angle_coeff @angle:hp-p5-hp harmonic 34.260 101.090 # SOURCE3 4 1.3036 + angle_coeff @angle:hp-p5-n1 harmonic 49.690 101.320 # HF/6-31G* 1 + angle_coeff @angle:hp-p5-o harmonic 48.280 116.580 # SOURCE3 7 1.3282 + angle_coeff @angle:hp-p5-oh harmonic 48.850 101.450 # SOURCE3 5 0.9084 + angle_coeff @angle:hp-p5-s harmonic 52.540 119.200 # SOURCE2 1 0.0000 + angle_coeff @angle:i-p5-i harmonic 57.350 107.170 # SOURCE3 1 0.0000 + angle_coeff @angle:i-p5-o harmonic 52.720 115.930 # SOURCE3 3 0.0415 + angle_coeff @angle:i-p5-oh harmonic 56.650 102.260 # SOURCE3 4 1.9577 + angle_coeff @angle:n1-p5-n1 harmonic 73.170 101.550 # HF/6-31G* 1 + angle_coeff @angle:n1-p5-o harmonic 71.450 113.780 # HF/6-31G* 1 + angle_coeff @angle:n2-p5-n2 harmonic 70.250 106.340 # SOURCE3 1 + angle_coeff @angle:n2-p5-o harmonic 70.800 113.530 # SOURCE3 1 + angle_coeff @angle:n2-p5-oh harmonic 71.420 102.400 # SOURCE3 1 + angle_coeff @angle:n3-p5-n3 harmonic 68.510 103.370 # SOURCE4 47 2.1009 + angle_coeff @angle:n3-p5-nh harmonic 68.130 104.020 # SOURCE4 5 1.8740 + angle_coeff @angle:n3-p5-o harmonic 68.760 114.640 # SOURCE4 76 2.2728 + angle_coeff @angle:n3-p5-oh harmonic 69.420 104.180 # SOURCE3 6 0.4373 + angle_coeff @angle:n3-p5-os harmonic 70.640 101.940 # SOURCE4 34 2.3553 + angle_coeff @angle:n3-p5-s harmonic 78.990 117.120 # SOURCE4 7 0.7109 + angle_coeff @angle:n4-p5-n4 harmonic 62.620 102.200 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-p5-o harmonic 65.690 109.780 # SOURCE3 5 2.7519 + angle_coeff @angle:n4-p5-oh harmonic 67.490 98.480 # SOURCE3 6 0.4104 + angle_coeff @angle:n4-p5-os harmonic 69.210 94.550 # SOURCE3 2 0.0000 + angle_coeff @angle:na-p5-na harmonic 64.830 108.570 # SOURCE3 1 0.0000 + angle_coeff @angle:na-p5-o harmonic 67.730 113.430 # SOURCE3 11 0.8968 + angle_coeff @angle:na-p5-oh harmonic 68.960 102.070 # SOURCE3 16 1.4144 + angle_coeff @angle:na-p5-os harmonic 69.040 103.060 # SOURCE3 4 0.7463 + angle_coeff @angle:nh-p5-nh harmonic 69.500 99.510 # SOURCE3 1 0.0000 + angle_coeff @angle:nh-p5-o harmonic 67.300 118.910 # SOURCE3 3 1.3237 + angle_coeff @angle:nh-p5-oh harmonic 69.360 103.810 # SOURCE3 2 0.0000 + angle_coeff @angle:nh-p5-os harmonic 70.950 100.510 # SOURCE3 2 0.0000 + angle_coeff @angle:n-p5-n3 harmonic 67.330 104.110 # SOURCE4 11 1.4088 + angle_coeff @angle:n-p5-n harmonic 66.800 103.090 # SOURCE3 1 0.0000 + angle_coeff @angle:n-p5-o harmonic 69.370 108.730 # SOURCE4 5 0.2571 + angle_coeff @angle:n-p5-oh harmonic 68.990 102.440 # SOURCE3 4 0.0999 + angle_coeff @angle:no-p5-no harmonic 64.570 95.680 # SOURCE3 1 0.0000 + angle_coeff @angle:no-p5-o harmonic 64.720 112.750 # SOURCE3 4 3.3684 + angle_coeff @angle:no-p5-oh harmonic 66.430 101.350 # SOURCE3 2 0.0000 + angle_coeff @angle:no-p5-os harmonic 66.640 101.700 # SOURCE3 4 0.0565 + angle_coeff @angle:n-p5-os harmonic 70.090 100.480 # SOURCE3 2 0.0000 + angle_coeff @angle:oh-p5-oh harmonic 71.250 102.450 # SOURCE3 39 2.4223 + angle_coeff @angle:oh-p5-os harmonic 71.770 102.370 # SOURCE3 8 1.5063 + angle_coeff @angle:oh-p5-p2 harmonic 60.920 103.530 # SOURCE3 1 + angle_coeff @angle:oh-p5-p3 harmonic 60.040 103.830 # SOURCE3 13 0.4303 + angle_coeff @angle:oh-p5-p4 harmonic 60.070 101.790 # SOURCE3 1 + angle_coeff @angle:oh-p5-p5 harmonic 64.950 100.450 # SOURCE3 1 + angle_coeff @angle:oh-p5-s4 harmonic 81.520 103.240 # SOURCE3 1 + angle_coeff @angle:oh-p5-s6 harmonic 82.230 101.480 # SOURCE3 1 + angle_coeff @angle:oh-p5-s harmonic 85.370 102.880 # SOURCE3 3 1.6044 + angle_coeff @angle:oh-p5-sh harmonic 80.940 101.410 # SOURCE3 2 0.0000 + angle_coeff @angle:oh-p5-ss harmonic 78.780 104.330 # SOURCE3 6 2.0112 + angle_coeff @angle:o-p5-o harmonic 73.530 115.800 # SOURCE3 17 5.7902 + angle_coeff @angle:o-p5-oh harmonic 69.980 115.260 # SOURCE4 740 1.3004 + angle_coeff @angle:o-p5-os harmonic 70.340 116.090 # SOURCE3 35 3.2062 + angle_coeff @angle:o-p5-p2 harmonic 58.380 114.600 # SOURCE3 1 + angle_coeff @angle:o-p5-p3 harmonic 57.310 115.480 # SOURCE3 9 2.1084 + angle_coeff @angle:o-p5-p4 harmonic 56.910 114.660 # SOURCE3 1 + angle_coeff @angle:o-p5-p5 harmonic 62.020 113.440 # SOURCE3 1 + angle_coeff @angle:o-p5-s4 harmonic 80.110 110.230 # SOURCE3 1 + angle_coeff @angle:o-p5-s6 harmonic 79.570 111.750 # SOURCE3 1 + angle_coeff @angle:o-p5-s harmonic 81.840 116.940 # SOURCE3 3 2.9506 + angle_coeff @angle:o-p5-sh harmonic 77.150 114.560 # SOURCE3 3 1.7645 + angle_coeff @angle:os-p5-os harmonic 72.510 101.770 # SOURCE4 243 2.0816 + angle_coeff @angle:os-p5-p3 harmonic 60.190 103.670 # SOURCE3 2 0.0000 + angle_coeff @angle:os-p5-p5 harmonic 63.870 104.480 # SOURCE3 1 + angle_coeff @angle:os-p5-s4 harmonic 82.050 102.520 # SOURCE3 1 + angle_coeff @angle:os-p5-s6 harmonic 82.310 101.890 # SOURCE3 1 + angle_coeff @angle:o-p5-ss harmonic 76.760 112.460 # SOURCE3 6 2.7392 + angle_coeff @angle:os-p5-s harmonic 80.280 117.280 # SOURCE4 74 0.7542 + angle_coeff @angle:os-p5-sh harmonic 79.910 104.590 # SOURCE3 2 0.0000 + angle_coeff @angle:os-p5-ss harmonic 79.620 102.650 # SOURCE4 25 1.8093 + angle_coeff @angle:p2-p5-p2 harmonic 57.260 107.140 # SOURCE3 1 + angle_coeff @angle:p3-p5-p3 harmonic 56.920 105.230 # SOURCE3 3 5.1024 + angle_coeff @angle:p4-p5-p4 harmonic 57.300 101.620 # SOURCE3 1 + angle_coeff @angle:p5-p5-p5 harmonic 59.250 112.720 # SOURCE3 1 + angle_coeff @angle:s6-p5-s6 harmonic 98.920 105.180 # SOURCE3 1 + angle_coeff @angle:sh-p5-sh harmonic 97.210 104.560 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-p5-ss harmonic 95.280 107.130 # SOURCE3 1 + angle_coeff @angle:s-p5-s harmonic 100.790 114.130 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-p5-ss harmonic 93.470 109.610 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-pc-n harmonic 68.330 90.800 # SOURCE3 3 2.3423 + angle_coeff @angle:cd-pc-na harmonic 68.730 90.180 # SOURCE3 81 2.7619 + angle_coeff @angle:cc-pd-n harmonic 68.330 90.800 # SOURCE3 3 same_as_cd-pc-n + angle_coeff @angle:cc-pd-na harmonic 68.730 90.180 # SOURCE3 81 same_as_cd-pc-na + angle_coeff @angle:c2-pe-ca harmonic 62.070 101.440 # SOURCE3 3 0.7177 + angle_coeff @angle:c2-pe-ce harmonic 61.820 103.010 # SOURCE3 4 1.4470 + angle_coeff @angle:c2-pe-cg harmonic 65.280 104.030 # SOURCE3 3 3.8740 + angle_coeff @angle:c2-pe-n2 harmonic 71.820 94.140 # SOURCE3 1 + angle_coeff @angle:c2-pe-ne harmonic 66.880 98.700 # SOURCE3 12 5.3383 + angle_coeff @angle:c2-pe-o harmonic 65.620 115.160 # SOURCE3 2 0.0149 + angle_coeff @angle:c2-pe-p2 harmonic 64.330 107.820 # SOURCE3 1 + angle_coeff @angle:c2-pe-pe harmonic 60.830 102.990 # SOURCE3 9 8.2860 + angle_coeff @angle:c2-pe-px harmonic 64.550 97.370 # SOURCE3 4 0.6655 + angle_coeff @angle:c2-pe-py harmonic 64.310 96.710 # SOURCE3 4 1.2755 + angle_coeff @angle:c2-pe-s harmonic 83.060 111.160 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-pe-sx harmonic 77.900 95.110 # SOURCE3 4 0.2676 + angle_coeff @angle:c2-pe-sy harmonic 76.420 95.560 # SOURCE3 2 0.0462 + angle_coeff @angle:ca-pe-n2 harmonic 65.480 102.030 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-pe-o harmonic 64.570 106.880 # SOURCE3 2 0.0018 + angle_coeff @angle:ca-pe-p2 harmonic 64.350 100.790 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-pe-pf harmonic 61.170 99.700 # SOURCE3 2 0.0000 + angle_coeff @angle:ca-pe-s harmonic 81.050 107.930 # SOURCE3 1 0.0000 + angle_coeff @angle:c-pe-c2 harmonic 61.660 97.300 # SOURCE3 3 0.0335 + angle_coeff @angle:ce-pe-n2 harmonic 66.250 100.550 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-pe-o harmonic 64.690 107.440 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-pe-p2 harmonic 64.930 99.560 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-pe-s harmonic 82.230 105.540 # SOURCE3 1 0.0000 + angle_coeff @angle:cg-pe-n2 harmonic 70.820 101.790 # SOURCE3 1 0.0000 + angle_coeff @angle:cg-pe-o harmonic 69.640 107.620 # SOURCE3 1 0.0000 + angle_coeff @angle:cg-pe-p2 harmonic 66.260 104.680 # SOURCE3 2 5.1435 + angle_coeff @angle:cg-pe-s harmonic 85.560 108.600 # SOURCE3 4 2.6981 + angle_coeff @angle:n2-pe-n2 harmonic 72.340 108.140 # SOURCE3 1 + angle_coeff @angle:n2-pe-ne harmonic 68.550 106.800 # SOURCE3 6 4.5981 + angle_coeff @angle:n2-pe-o harmonic 70.860 115.390 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-pe-p2 harmonic 66.740 111.600 # SOURCE3 1 + angle_coeff @angle:n2-pe-pe harmonic 61.500 109.400 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-pe-px harmonic 63.500 110.300 # SOURCE3 3 6.0548 + angle_coeff @angle:n2-pe-py harmonic 68.340 93.680 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-pe-s harmonic 86.860 114.840 # SOURCE3 3 3.6512 + angle_coeff @angle:n2-pe-sx harmonic 79.730 97.830 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-pe-sy harmonic 78.100 98.140 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-pe-o harmonic 68.170 110.240 # SOURCE3 3 3.8478 + angle_coeff @angle:ne-pe-p2 harmonic 66.630 104.480 # SOURCE3 2 7.1207 + angle_coeff @angle:ne-pe-s harmonic 85.380 109.190 # SOURCE3 5 3.6708 + angle_coeff @angle:o-pe-o harmonic 70.340 119.960 # SOURCE3 1 0.0000 + angle_coeff @angle:o-pe-p2 harmonic 66.560 114.230 # SOURCE3 1 0.0000 + angle_coeff @angle:o-pe-pe harmonic 53.630 145.960 # SOURCE3 1 0.0000 + angle_coeff @angle:o-pe-px harmonic 65.790 104.370 # SOURCE3 1 0.0000 + angle_coeff @angle:o-pe-py harmonic 65.210 104.490 # SOURCE3 1 0.0000 + angle_coeff @angle:o-pe-s harmonic 86.750 117.420 # SOURCE3 2 0.0426 + angle_coeff @angle:o-pe-sx harmonic 76.900 106.590 # SOURCE3 1 0.0000 + angle_coeff @angle:o-pe-sy harmonic 75.980 105.040 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-pe-pe harmonic 65.430 98.240 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-pe-px harmonic 63.970 108.280 # SOURCE3 2 6.2959 + angle_coeff @angle:p2-pe-py harmonic 62.850 110.870 # SOURCE3 3 8.1645 + angle_coeff @angle:p2-pe-s harmonic 85.370 111.280 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-pe-sx harmonic 81.920 95.730 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-pe-sy harmonic 80.670 95.950 # SOURCE3 1 0.0000 + angle_coeff @angle:pe-pe-s harmonic 80.550 107.910 # SOURCE3 2 1.5577 + angle_coeff @angle:px-pe-s harmonic 83.060 107.620 # SOURCE3 2 3.7266 + angle_coeff @angle:py-pe-s harmonic 82.090 108.730 # SOURCE3 3 5.3201 + angle_coeff @angle:s-pe-s harmonic 88.130 178.440 # SOURCE3 1 0.0000 + angle_coeff @angle:s-pe-sx harmonic 99.120 108.320 # SOURCE3 2 3.0318 + angle_coeff @angle:s-pe-sy harmonic 98.190 106.930 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-pf-ca harmonic 62.070 101.440 # SOURCE3 3 same_as_c2-pe-ca + angle_coeff @angle:c2-pf-cf harmonic 61.820 103.010 # SOURCE3 4 same_as_c2-pe-ce + angle_coeff @angle:c2-pf-ch harmonic 65.280 104.030 # SOURCE3 3 same_as_c2-pe-cg + angle_coeff @angle:c2-pf-n2 harmonic 71.820 94.140 # SOURCE3 1 same_as_c2-pe-n2 + angle_coeff @angle:c2-pf-nf harmonic 66.880 98.700 # SOURCE3 12 same_as_c2-pe-ne + angle_coeff @angle:c2-pf-o harmonic 65.620 115.160 # SOURCE3 2 same_as_c2-pe-o + angle_coeff @angle:c2-pf-p2 harmonic 64.330 107.820 # SOURCE3 1 same_as_c2-pe-p2 + angle_coeff @angle:c2-pf-pf harmonic 60.830 102.990 # SOURCE3 9 same_as_c2-pe-pe + angle_coeff @angle:c2-pf-px harmonic 64.550 97.370 # SOURCE3 4 same_as_c2-pe-px + angle_coeff @angle:c2-pf-py harmonic 64.310 96.710 # SOURCE3 4 same_as_c2-pe-py + angle_coeff @angle:c2-pf-s harmonic 83.060 111.160 # SOURCE3 2 same_as_c2-pe-s + angle_coeff @angle:c2-pf-sx harmonic 77.900 95.110 # SOURCE3 4 same_as_c2-pe-sx + angle_coeff @angle:c2-pf-sy harmonic 76.420 95.560 # SOURCE3 2 same_as_c2-pe-sy + angle_coeff @angle:ca-pf-n2 harmonic 65.480 102.030 # SOURCE3 1 same_as_ca-pe-n2 + angle_coeff @angle:ca-pf-o harmonic 64.570 106.880 # SOURCE3 2 same_as_ca-pe-o + angle_coeff @angle:ca-pf-p2 harmonic 64.350 100.790 # SOURCE3 1 same_as_ca-pe-p2 + angle_coeff @angle:ca-pf-pe harmonic 61.170 99.700 # SOURCE3 2 0.0000 + angle_coeff @angle:ca-pf-s harmonic 81.050 107.930 # SOURCE3 1 same_as_ca-pe-s + angle_coeff @angle:c-pf-c2 harmonic 61.660 97.300 # SOURCE3 3 same_as_c-pe-c2 + angle_coeff @angle:cf-pf-n2 harmonic 66.250 100.550 # SOURCE3 1 same_as_ce-pe-n2 + angle_coeff @angle:cf-pf-o harmonic 64.690 107.440 # SOURCE3 1 same_as_ce-pe-o + angle_coeff @angle:cf-pf-p2 harmonic 64.930 99.560 # SOURCE3 1 same_as_ce-pe-p2 + angle_coeff @angle:cf-pf-s harmonic 82.230 105.540 # SOURCE3 1 same_as_ce-pe-s + angle_coeff @angle:ch-pf-n2 harmonic 70.820 101.790 # SOURCE3 1 same_as_cg-pe-n2 + angle_coeff @angle:ch-pf-o harmonic 69.640 107.620 # SOURCE3 1 same_as_cg-pe-o + angle_coeff @angle:ch-pf-p2 harmonic 66.260 104.680 # SOURCE3 2 same_as_cg-pe-p2 + angle_coeff @angle:ch-pf-s harmonic 85.560 108.600 # SOURCE3 4 same_as_cg-pe-s + angle_coeff @angle:n2-pf-n2 harmonic 72.340 108.140 # SOURCE3 1 same_as_n2-pe-n2 + angle_coeff @angle:n2-pf-nf harmonic 68.550 106.800 # SOURCE3 6 same_as_n2-pe-ne + angle_coeff @angle:n2-pf-o harmonic 70.860 115.390 # SOURCE3 1 same_as_n2-pe-o + angle_coeff @angle:n2-pf-p2 harmonic 66.740 111.600 # SOURCE3 1 same_as_n2-pe-p2 + angle_coeff @angle:n2-pf-pf harmonic 61.500 109.400 # SOURCE3 1 same_as_n2-pe-pe + angle_coeff @angle:n2-pf-px harmonic 63.500 110.300 # SOURCE3 3 same_as_n2-pe-px + angle_coeff @angle:n2-pf-py harmonic 68.340 93.680 # SOURCE3 1 same_as_n2-pe-py + angle_coeff @angle:n2-pf-s harmonic 86.860 114.840 # SOURCE3 3 same_as_n2-pe-s + angle_coeff @angle:n2-pf-sx harmonic 79.730 97.830 # SOURCE3 1 same_as_n2-pe-sx + angle_coeff @angle:n2-pf-sy harmonic 78.100 98.140 # SOURCE3 1 same_as_n2-pe-sy + angle_coeff @angle:nf-pf-o harmonic 68.170 110.240 # SOURCE3 3 same_as_ne-pe-o + angle_coeff @angle:nf-pf-p2 harmonic 66.630 104.480 # SOURCE3 2 same_as_ne-pe-p2 + angle_coeff @angle:nf-pf-s harmonic 85.380 109.190 # SOURCE3 5 same_as_ne-pe-s + angle_coeff @angle:o-pf-o harmonic 70.340 119.960 # SOURCE3 1 same_as_o-pe-o + angle_coeff @angle:o-pf-p2 harmonic 66.560 114.230 # SOURCE3 1 same_as_o-pe-p2 + angle_coeff @angle:o-pf-pf harmonic 53.630 145.960 # SOURCE3 1 same_as_o-pe-pe + angle_coeff @angle:o-pf-px harmonic 65.790 104.370 # SOURCE3 1 same_as_o-pe-px + angle_coeff @angle:o-pf-py harmonic 65.210 104.490 # SOURCE3 1 same_as_o-pe-py + angle_coeff @angle:o-pf-s harmonic 86.750 117.420 # SOURCE3 2 same_as_o-pe-s + angle_coeff @angle:o-pf-sx harmonic 76.900 106.590 # SOURCE3 1 same_as_o-pe-sx + angle_coeff @angle:o-pf-sy harmonic 75.980 105.040 # SOURCE3 1 same_as_o-pe-sy + angle_coeff @angle:p2-pf-pf harmonic 65.430 98.240 # SOURCE3 1 same_as_p2-pe-pe + angle_coeff @angle:p2-pf-px harmonic 63.970 108.280 # SOURCE3 2 same_as_p2-pe-px + angle_coeff @angle:p2-pf-py harmonic 62.850 110.870 # SOURCE3 3 same_as_p2-pe-py + angle_coeff @angle:p2-pf-s harmonic 85.370 111.280 # SOURCE3 1 same_as_p2-pe-s + angle_coeff @angle:p2-pf-sx harmonic 81.920 95.730 # SOURCE3 1 same_as_p2-pe-sx + angle_coeff @angle:p2-pf-sy harmonic 80.670 95.950 # SOURCE3 1 same_as_p2-pe-sy + angle_coeff @angle:pf-pf-s harmonic 80.550 107.910 # SOURCE3 2 same_as_pe-pe-s + angle_coeff @angle:px-pf-s harmonic 83.060 107.620 # SOURCE3 2 same_as_px-pe-s + angle_coeff @angle:py-pf-s harmonic 82.090 108.730 # SOURCE3 3 same_as_py-pe-s + angle_coeff @angle:s-pf-s harmonic 88.130 178.440 # SOURCE3 1 same_as_s-pe-s + angle_coeff @angle:s-pf-sx harmonic 99.120 108.320 # SOURCE3 2 same_as_s-pe-sx + angle_coeff @angle:s-pf-sy harmonic 98.190 106.930 # SOURCE3 1 same_as_s-pe-sy + angle_coeff @angle:c3-px-ca harmonic 59.090 104.790 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-px-ce harmonic 59.140 104.860 # SOURCE3 4 0.6354 + angle_coeff @angle:c3-px-cf harmonic 59.140 104.860 # SOURCE3 4 same_as_c3-px-ce + angle_coeff @angle:c3-px-ne harmonic 63.210 102.460 # SOURCE3 7 1.8685 + angle_coeff @angle:c3-px-nf harmonic 63.210 102.460 # SOURCE3 7 same_as_c3-px-ne + angle_coeff @angle:c3-px-o harmonic 62.960 113.680 # SOURCE3 28 4.8990 + angle_coeff @angle:c3-px-pe harmonic 60.390 105.730 # SOURCE3 10 4.4059 + angle_coeff @angle:c3-px-pf harmonic 60.390 105.730 # SOURCE3 10 same_as_c3-px-pe + angle_coeff @angle:c3-px-py harmonic 57.460 103.110 # SOURCE3 3 0.8680 + angle_coeff @angle:c3-px-sx harmonic 72.950 99.550 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-px-sy harmonic 71.410 103.410 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-px-ca harmonic 59.260 104.150 # SOURCE3 2 3.6168 + angle_coeff @angle:ca-px-o harmonic 64.720 107.500 # SOURCE3 5 5.7355 + angle_coeff @angle:c-px-c3 harmonic 58.650 101.720 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-px-ce harmonic 59.370 104.210 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-px-o harmonic 63.000 113.790 # SOURCE3 6 0.3877 + angle_coeff @angle:cf-px-cf harmonic 59.370 104.210 # SOURCE3 1 same_as_ce-px-ce + angle_coeff @angle:cf-px-o harmonic 63.000 113.790 # SOURCE3 6 same_as_ce-px-o + angle_coeff @angle:c-px-o harmonic 60.710 114.470 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-px-ne harmonic 66.990 103.220 # SOURCE3 2 0.6807 + angle_coeff @angle:ne-px-o harmonic 67.560 114.130 # SOURCE3 11 8.9737 + angle_coeff @angle:nf-px-nf harmonic 66.990 103.220 # SOURCE3 2 same_as_ne-px-ne + angle_coeff @angle:nf-px-o harmonic 67.560 114.130 # SOURCE3 11 same_as_ne-px-o + angle_coeff @angle:o-px-pe harmonic 62.400 116.500 # SOURCE3 12 8.2925 + angle_coeff @angle:o-px-pf harmonic 62.400 116.500 # SOURCE3 12 same_as_o-px-pe + angle_coeff @angle:o-px-py harmonic 57.960 114.200 # SOURCE3 5 1.7165 + angle_coeff @angle:o-px-sx harmonic 72.440 112.810 # SOURCE3 3 0.8799 + angle_coeff @angle:o-px-sy harmonic 71.990 113.540 # SOURCE3 3 0.5010 + angle_coeff @angle:pe-px-pe harmonic 61.250 110.710 # SOURCE3 1 0.0000 + angle_coeff @angle:pf-px-pf harmonic 61.250 110.710 # SOURCE3 1 same_as_pe-px-pe + angle_coeff @angle:py-px-py harmonic 56.600 107.780 # SOURCE3 1 0.0000 + angle_coeff @angle:sx-px-sx harmonic 94.100 96.240 # SOURCE3 1 0.0000 + angle_coeff @angle:sy-px-sy harmonic 90.960 102.360 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-py-n4 harmonic 59.670 103.830 # SOURCE3 4 0.0000 + angle_coeff @angle:c3-py-na harmonic 61.950 106.890 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-py-o harmonic 62.250 117.870 # SOURCE3 13 2.3554 + angle_coeff @angle:c3-py-oh harmonic 65.880 100.160 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-py-os harmonic 64.170 105.390 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-py-px harmonic 56.690 106.270 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-py-py harmonic 54.980 113.970 # SOURCE3 10 1.6346 + angle_coeff @angle:c3-py-sx harmonic 70.270 106.360 # SOURCE3 4 0.0000 + angle_coeff @angle:ca-py-ca harmonic 59.130 107.550 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-py-o harmonic 63.640 113.980 # SOURCE3 3 0.5309 + angle_coeff @angle:ca-py-oh harmonic 65.370 102.680 # SOURCE4 5 1.2945 + angle_coeff @angle:ca-py-os harmonic 64.980 103.750 # SOURCE3 2 0.0000 + angle_coeff @angle:c-py-c3 harmonic 57.070 110.360 # SOURCE3 1 0.0000 + angle_coeff @angle:c-py-c harmonic 57.910 104.200 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-py-ce harmonic 59.600 106.540 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-py-o harmonic 64.310 112.160 # SOURCE3 5 3.2594 + angle_coeff @angle:ce-py-oh harmonic 64.850 104.770 # SOURCE3 6 2.1852 + angle_coeff @angle:ce-py-os harmonic 65.240 103.340 # SOURCE3 2 0.0000 + angle_coeff @angle:cf-py-cf harmonic 59.600 106.540 # SOURCE3 1 same_as_ce-py-ce + angle_coeff @angle:cf-py-o harmonic 64.310 112.160 # SOURCE3 5 same_as_ce-py-o + angle_coeff @angle:cf-py-oh harmonic 64.850 104.770 # SOURCE3 6 same_as_ce-py-oh + angle_coeff @angle:cf-py-os harmonic 65.240 103.340 # SOURCE3 2 same_as_ce-py-os + angle_coeff @angle:c-py-o harmonic 61.560 115.250 # SOURCE3 6 2.6519 + angle_coeff @angle:c-py-oh harmonic 63.980 102.140 # SOURCE3 6 1.0654 + angle_coeff @angle:c-py-os harmonic 66.040 95.740 # SOURCE3 3 9.0999 + angle_coeff @angle:n3-py-ne harmonic 67.010 108.440 # SOURCE4 12 0.9498 + angle_coeff @angle:n4-py-o harmonic 62.060 115.580 # SOURCE3 4 0.0000 + angle_coeff @angle:n4-py-py harmonic 79.860 55.100 # SOURCE3 4 0.0000 + angle_coeff @angle:na-py-o harmonic 65.180 122.400 # SOURCE3 2 0.0000 + angle_coeff @angle:na-py-py harmonic 85.440 50.880 # SOURCE3 2 0.0000 + angle_coeff @angle:ne-py-ne harmonic 69.540 106.290 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-py-o harmonic 70.320 113.210 # SOURCE3 15 3.8894 + angle_coeff @angle:ne-py-oh harmonic 70.530 104.700 # SOURCE3 26 2.7513 + angle_coeff @angle:ne-py-os harmonic 71.610 101.330 # SOURCE3 2 0.0000 + angle_coeff @angle:nf-py-nf harmonic 69.540 106.290 # SOURCE3 1 same_as_ne-py-ne + angle_coeff @angle:nf-py-o harmonic 70.320 113.210 # SOURCE3 15 same_as_ne-py-o + angle_coeff @angle:nf-py-oh harmonic 70.530 104.700 # SOURCE3 26 same_as_ne-py-oh + angle_coeff @angle:nf-py-os harmonic 71.610 101.330 # SOURCE3 2 same_as_ne-py-os + angle_coeff @angle:oh-py-oh harmonic 72.010 101.780 # SOURCE3 35 2.2937 + angle_coeff @angle:oh-py-pe harmonic 64.390 104.840 # SOURCE3 22 2.0337 + angle_coeff @angle:oh-py-pf harmonic 64.390 104.840 # SOURCE3 22 same_as_oh-py-pe + angle_coeff @angle:oh-py-px harmonic 60.300 104.300 # SOURCE3 8 1.2772 + angle_coeff @angle:oh-py-py harmonic 61.760 100.450 # SOURCE3 6 0.0000 + angle_coeff @angle:oh-py-sx harmonic 75.730 100.940 # SOURCE3 4 0.0000 + angle_coeff @angle:oh-py-sy harmonic 77.890 101.470 # SOURCE3 6 0.2490 + angle_coeff @angle:o-py-oh harmonic 69.900 116.140 # SOURCE3 79 2.1455 + angle_coeff @angle:o-py-os harmonic 69.600 116.790 # SOURCE3 17 1.3534 + angle_coeff @angle:o-py-pe harmonic 62.460 114.560 # SOURCE3 12 3.6114 + angle_coeff @angle:o-py-pf harmonic 62.460 114.560 # SOURCE3 12 same_as_o-py-pe + angle_coeff @angle:o-py-px harmonic 58.710 111.370 # SOURCE3 5 0.3803 + angle_coeff @angle:o-py-py harmonic 56.790 120.430 # SOURCE3 16 6.0629 + angle_coeff @angle:os-py-os harmonic 72.020 101.250 # SOURCE3 8 2.0860 + angle_coeff @angle:os-py-py harmonic 60.540 104.480 # SOURCE3 4 0.0000 + angle_coeff @angle:os-py-sx harmonic 74.640 103.860 # SOURCE3 2 0.0000 + angle_coeff @angle:os-py-sy harmonic 77.620 102.120 # SOURCE3 2 0.0000 + angle_coeff @angle:o-py-sx harmonic 70.140 118.560 # SOURCE3 7 6.2976 + angle_coeff @angle:o-py-sy harmonic 74.750 111.710 # SOURCE3 5 1.1937 + angle_coeff @angle:pe-py-pe harmonic 61.640 107.140 # SOURCE3 1 0.0000 + angle_coeff @angle:pf-py-pf harmonic 61.640 107.140 # SOURCE3 1 same_as_pe-py-pe + angle_coeff @angle:py-py-py harmonic 55.680 112.700 # SOURCE3 1 0.0000 + angle_coeff @angle:py-py-sx harmonic 93.740 61.540 # SOURCE3 4 0.0000 + angle_coeff @angle:sy-py-sy harmonic 92.490 105.170 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-s2-o harmonic 41.150 117.250 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-s2-n2 harmonic 42.960 110.840 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-s2-o harmonic 41.410 114.700 # SOURCE2 1 0.0000 + angle_coeff @angle:cl-s2-n1 harmonic 35.940 117.700 # SOURCE2 1 0.0000 + angle_coeff @angle:f-s2-n1 harmonic 41.390 116.900 # SOURCE2 1 0.0000 + angle_coeff @angle:n1-s2-o harmonic 45.710 108.460 # HF/6-31G* 1 + angle_coeff @angle:n2-s2-o harmonic 42.500 121.200 # SOURCE2 2 0.8000 + angle_coeff @angle:o-s2-o harmonic 42.540 116.170 # SOURCE3 1 0.0000 + angle_coeff @angle:o-s2-s harmonic 50.510 118.300 # SOURCE2 1 0.0000 + angle_coeff @angle:s-s2-s harmonic 63.640 115.040 # SOURCE3 1 0.0000 + angle_coeff @angle:br-s4-br harmonic 40.430 98.020 # SOURCE3 1 + angle_coeff @angle:br-s4-c3 harmonic 38.910 92.980 # SOURCE3 1 0.0000 + angle_coeff @angle:br-s4-o harmonic 37.040 112.070 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-s4-c1 harmonic 40.890 93.550 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-s4-o harmonic 41.280 110.360 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-s4-c2 harmonic 38.790 102.290 # SOURCE3 1 + angle_coeff @angle:c2-s4-c3 harmonic 39.720 94.950 # SOURCE3 1 + angle_coeff @angle:c2-s4-o harmonic 41.680 107.090 # SOURCE3 1 + angle_coeff @angle:c3-s4-c3 harmonic 38.840 96.820 # SOURCE3 11 1.5580 + angle_coeff @angle:c3-s4-ca harmonic 39.410 95.000 # SOURCE3 1 + angle_coeff @angle:c3-s4-f harmonic 41.500 91.700 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s4-hs harmonic 29.130 90.600 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s4-i harmonic 33.080 90.530 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s4-n2 harmonic 43.220 90.590 # SOURCE3 1 + angle_coeff @angle:c3-s4-n3 harmonic 40.780 94.490 # SOURCE3 4 1.5570 + angle_coeff @angle:c3-s4-n harmonic 40.220 96.070 # SOURCE3 4 1.0354 + angle_coeff @angle:c3-s4-n4 harmonic 38.790 92.470 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s4-na harmonic 40.740 93.070 # SOURCE3 10 1.8813 + angle_coeff @angle:c3-s4-nh harmonic 40.360 97.080 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s4-no harmonic 39.130 89.530 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s4-o harmonic 41.060 106.210 # SOURCE3 60 2.0426 + angle_coeff @angle:c3-s4-oh harmonic 42.680 90.250 # SOURCE4 8 0.3023 + angle_coeff @angle:c3-s4-os harmonic 42.690 90.060 # SOURCE3 4 0.4484 + angle_coeff @angle:c3-s4-p2 harmonic 37.780 94.370 # SOURCE3 1 + angle_coeff @angle:c3-s4-p3 harmonic 38.650 96.540 # SOURCE3 4 1.3634 + angle_coeff @angle:c3-s4-p4 harmonic 36.430 97.400 # SOURCE3 1 + angle_coeff @angle:c3-s4-p5 harmonic 38.720 99.180 # SOURCE3 1 + angle_coeff @angle:c3-s4-s4 harmonic 50.930 89.500 # SOURCE3 1 + angle_coeff @angle:c3-s4-s harmonic 48.550 98.720 # SOURCE3 2 0.0185 + angle_coeff @angle:c3-s4-s6 harmonic 48.800 97.480 # SOURCE3 1 + angle_coeff @angle:c3-s4-sh harmonic 48.100 94.660 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s4-ss harmonic 47.970 95.310 # SOURCE3 3 1.4101 + angle_coeff @angle:ca-s4-ca harmonic 39.580 95.210 # SOURCE3 1 + angle_coeff @angle:ca-s4-o harmonic 41.300 106.630 # SOURCE3 1 + angle_coeff @angle:c-s4-c3 harmonic 38.500 95.070 # SOURCE3 1 + angle_coeff @angle:c-s4-c harmonic 39.630 86.830 # SOURCE3 1 + angle_coeff @angle:cl-s4-cl harmonic 38.990 97.680 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-s4-o harmonic 39.110 108.340 # SOURCE3 2 0.0000 + angle_coeff @angle:c-s4-o harmonic 40.030 106.170 # SOURCE3 1 + angle_coeff @angle:cx-s4-cx harmonic 54.250 48.800 # SOURCE2 1 0.0000 + angle_coeff @angle:cx-s4-o harmonic 40.110 110.000 # SOURCE2 1 0.0000 + angle_coeff @angle:f-s4-f harmonic 43.790 92.710 # SOURCE2 3 0.1490 + angle_coeff @angle:f-s4-o harmonic 43.870 106.810 # SOURCE2 2 0.0100 + angle_coeff @angle:f-s4-s harmonic 47.340 107.500 # SOURCE2 1 0.0000 + angle_coeff @angle:hs-s4-hs harmonic 23.650 87.000 # SOURCE3 2 0.0202 + angle_coeff @angle:hs-s4-n1 harmonic 32.050 90.510 # HF/6-31G* 1 + angle_coeff @angle:hs-s4-o harmonic 31.160 110.270 # SOURCE3 5 0.1908 + angle_coeff @angle:i-s4-i harmonic 34.070 97.290 # SOURCE3 1 + angle_coeff @angle:i-s4-o harmonic 29.610 113.910 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-s4-n1 harmonic 45.300 94.020 # HF/6-31G* 1 + angle_coeff @angle:n1-s4-o harmonic 43.950 110.090 # HF/6-31G* 1 + angle_coeff @angle:n2-s4-n2 harmonic 47.410 90.170 # SOURCE3 1 + angle_coeff @angle:n2-s4-o harmonic 45.130 107.570 # SOURCE3 1 + angle_coeff @angle:n3-s4-n3 harmonic 43.100 91.190 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-s4-o harmonic 42.290 109.070 # SOURCE3 6 2.3605 + angle_coeff @angle:n4-s4-n4 harmonic 37.790 94.610 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-s4-o harmonic 39.520 104.910 # SOURCE3 3 0.4370 + angle_coeff @angle:na-s4-na harmonic 39.810 103.100 # SOURCE3 1 + angle_coeff @angle:na-s4-o harmonic 41.620 109.750 # SOURCE3 10 2.6919 + angle_coeff @angle:nh-s4-nh harmonic 43.150 92.240 # SOURCE3 1 0.0000 + angle_coeff @angle:nh-s4-o harmonic 42.790 107.540 # SOURCE3 3 0.0401 + angle_coeff @angle:n-s4-n harmonic 42.570 91.300 # SOURCE3 1 + angle_coeff @angle:n-s4-o harmonic 42.600 105.700 # SOURCE3 4 1.6857 + angle_coeff @angle:no-s4-no harmonic 39.760 83.400 # SOURCE3 1 0.0000 + angle_coeff @angle:no-s4-o harmonic 39.370 103.580 # SOURCE3 3 1.5109 + angle_coeff @angle:oh-s4-oh harmonic 43.170 100.340 # SOURCE3 1 + angle_coeff @angle:o-s4-o harmonic 46.570 110.610 # SOURCE3 5 3.6413 + angle_coeff @angle:o-s4-oh harmonic 43.430 110.130 # SOURCE4 10 0.5760 + angle_coeff @angle:o-s4-os harmonic 43.590 109.020 # SOURCE3 8 1.5005 + angle_coeff @angle:o-s4-p2 harmonic 37.660 106.770 # SOURCE3 1 + angle_coeff @angle:o-s4-p3 harmonic 39.430 106.510 # SOURCE3 8 4.0943 + angle_coeff @angle:o-s4-p4 harmonic 37.270 103.360 # SOURCE3 1 + angle_coeff @angle:o-s4-p5 harmonic 42.180 96.950 # SOURCE3 1 + angle_coeff @angle:o-s4-s4 harmonic 50.530 104.550 # SOURCE3 1 + angle_coeff @angle:o-s4-s harmonic 48.850 112.220 # SOURCE3 4 2.8682 + angle_coeff @angle:o-s4-s6 harmonic 50.940 102.840 # SOURCE3 1 + angle_coeff @angle:o-s4-sh harmonic 47.960 107.510 # SOURCE3 3 0.7511 + angle_coeff @angle:os-s4-os harmonic 44.590 93.680 # SOURCE3 2 2.4166 + angle_coeff @angle:o-s4-ss harmonic 47.560 109.490 # SOURCE3 5 1.8509 + angle_coeff @angle:p2-s4-p2 harmonic 38.360 92.620 # SOURCE3 1 + angle_coeff @angle:p3-s4-p3 harmonic 39.590 95.710 # SOURCE3 2 1.2239 + angle_coeff @angle:p5-s4-p5 harmonic 40.900 93.860 # SOURCE3 1 + angle_coeff @angle:s4-s4-s4 harmonic 65.560 90.170 # SOURCE3 1 + angle_coeff @angle:s4-s4-s6 harmonic 65.560 90.170 # SOURCE3 1 + angle_coeff @angle:s6-s4-s6 harmonic 64.380 93.520 # SOURCE3 1 + angle_coeff @angle:sh-s4-sh harmonic 58.920 102.760 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-s4-ss harmonic 58.980 102.640 # SOURCE3 1 + angle_coeff @angle:s-s4-s harmonic 60.000 108.080 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-s4-ss harmonic 61.190 95.470 # SOURCE3 1 0.0000 + angle_coeff @angle:br-s6-br harmonic 41.990 101.570 # SOURCE3 1 0.0000 + angle_coeff @angle:br-s6-c3 harmonic 39.570 98.990 # SOURCE3 1 0.0000 + angle_coeff @angle:br-s6-f harmonic 39.450 100.600 # SOURCE2 1 0.0000 + angle_coeff @angle:br-s6-o harmonic 39.980 107.580 # SOURCE3 6 0.3000 + angle_coeff @angle:c1-s6-c1 harmonic 40.100 99.990 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-s6-o harmonic 42.610 108.230 # SOURCE3 4 0.0000 + angle_coeff @angle:c2-s6-c2 harmonic 38.710 102.750 # SOURCE3 1 + angle_coeff @angle:c2-s6-c3 harmonic 38.310 104.050 # SOURCE3 1 + angle_coeff @angle:c2-s6-o harmonic 42.250 106.580 # SOURCE3 1 + angle_coeff @angle:c3-s6-c3 harmonic 38.390 102.830 # SOURCE3 7 1.2531 + angle_coeff @angle:c3-s6-ca harmonic 38.480 103.170 # SOURCE3 1 + angle_coeff @angle:c3-s6-cy harmonic 39.140 94.570 # SOURCE4 8 0.4183 + angle_coeff @angle:c3-s6-f harmonic 41.130 97.110 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s6-hs harmonic 28.120 100.620 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s6-i harmonic 31.800 97.740 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s6-n2 harmonic 39.680 112.950 # SOURCE4 11 0.7920 + angle_coeff @angle:c3-s6-n3 harmonic 41.120 101.380 # SOURCE4 60 0.9507 + angle_coeff @angle:c3-s6-n harmonic 39.940 102.970 # SOURCE3 4 0.8785 + angle_coeff @angle:c3-s6-n4 harmonic 38.370 99.400 # SOURCE3 3 0.4695 + angle_coeff @angle:c3-s6-na harmonic 39.840 102.810 # SOURCE3 10 3.1256 + angle_coeff @angle:c3-s6-nh harmonic 39.880 104.310 # SOURCE4 34 1.5848 + angle_coeff @angle:c3-s6-no harmonic 37.590 99.570 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s6-o harmonic 41.660 108.320 # SOURCE3 112 1.8014 + angle_coeff @angle:c3-s6-oh harmonic 42.370 98.600 # SOURCE4 42 0.8366 + angle_coeff @angle:c3-s6-os harmonic 42.970 96.320 # SOURCE4 30 0.4539 + angle_coeff @angle:c3-s6-p2 harmonic 35.860 106.470 # SOURCE3 1 + angle_coeff @angle:c3-s6-p3 harmonic 37.690 103.400 # SOURCE3 3 0.8516 + angle_coeff @angle:c3-s6-p4 harmonic 35.150 104.120 # SOURCE3 1 + angle_coeff @angle:c3-s6-p5 harmonic 38.150 103.460 # SOURCE3 1 + angle_coeff @angle:c3-s6-s4 harmonic 48.920 98.100 # SOURCE3 1 + angle_coeff @angle:c3-s6-s harmonic 48.070 104.500 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s6-s6 harmonic 47.990 101.950 # SOURCE3 1 + angle_coeff @angle:c3-s6-sh harmonic 47.570 101.840 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s6-ss harmonic 47.260 102.470 # SOURCE3 3 1.7451 + angle_coeff @angle:ca-s6-ca harmonic 38.670 103.080 # SOURCE3 1 + angle_coeff @angle:ca-s6-o harmonic 42.780 104.070 # SOURCE4 59 0.5636 + angle_coeff @angle:c-s6-c3 harmonic 37.620 101.240 # SOURCE3 1 + angle_coeff @angle:c-s6-c harmonic 36.960 99.820 # SOURCE3 1 + angle_coeff @angle:cc-s6-o harmonic 42.850 103.630 # SOURCE4 9 0.5934 + angle_coeff @angle:cl-s6-cl harmonic 38.290 101.250 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-s6-f harmonic 38.940 99.000 # SOURCE2 1 0.0000 + angle_coeff @angle:cl-s6-o harmonic 39.360 107.660 # SOURCE3 4 0.0000 + angle_coeff @angle:c-s6-o harmonic 40.020 107.970 # SOURCE3 1 + angle_coeff @angle:c-s6-os harmonic 40.270 102.120 # SOURCE3 1 + angle_coeff @angle:cx-s6-cx harmonic 53.940 54.700 # SOURCE2 1 0.0000 + angle_coeff @angle:cy-s6-o harmonic 39.940 110.220 # SOURCE4 20 1.1009 + angle_coeff @angle:f-s6-f harmonic 44.300 94.700 # SOURCE2 3 0.9899 + angle_coeff @angle:f-s6-o harmonic 45.290 106.480 # SOURCE3 2 0.0000 + angle_coeff @angle:hs-s6-hs harmonic 22.430 99.020 # SOURCE3 2 0.0595 + angle_coeff @angle:hs-s6-n1 harmonic 34.230 97.270 # HF/6-31G* 1 + angle_coeff @angle:hs-s6-o harmonic 32.480 107.600 # SOURCE3 10 0.0343 + angle_coeff @angle:i-s6-i harmonic 33.730 99.250 # SOURCE3 1 + angle_coeff @angle:i-s6-o harmonic 29.870 109.740 # SOURCE3 2 0.0000 + angle_coeff @angle:n1-s6-n1 harmonic 52.370 95.520 # HF/6-31G* 1 + angle_coeff @angle:n1-s6-o harmonic 49.300 107.520 # HF/6-31G* 1 + angle_coeff @angle:n2-s6-n2 harmonic 47.050 98.610 # SOURCE3 1 + angle_coeff @angle:n2-s6-o harmonic 45.100 116.410 # SOURCE3 3 5.0830 + angle_coeff @angle:n2-s6-oh harmonic 44.890 106.960 # SOURCE3 2 0.0000 + angle_coeff @angle:n2-s6-os harmonic 45.860 103.250 # SOURCE3 1 + angle_coeff @angle:n3-s6-n3 harmonic 44.730 98.570 # SOURCE4 7 0.2690 + angle_coeff @angle:n3-s6-o harmonic 45.610 106.800 # SOURCE3 14 1.7908 + angle_coeff @angle:n3-s6-os harmonic 45.580 99.260 # SOURCE4 8 0.5141 + angle_coeff @angle:n4-s6-n4 harmonic 37.520 101.850 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-s6-o harmonic 41.190 102.920 # SOURCE3 10 1.5434 + angle_coeff @angle:na-s6-na harmonic 42.390 98.040 # SOURCE3 1 + angle_coeff @angle:na-s6-o harmonic 44.090 105.670 # SOURCE3 20 0.8019 + angle_coeff @angle:nh-s6-nh harmonic 43.940 94.560 # SOURCE3 1 0.0000 + angle_coeff @angle:nh-s6-o harmonic 43.940 109.120 # SOURCE3 6 0.9556 + angle_coeff @angle:n-s6-n harmonic 41.410 104.160 # SOURCE3 1 + angle_coeff @angle:n-s6-o harmonic 44.260 105.910 # SOURCE3 8 0.2953 + angle_coeff @angle:no-s6-no harmonic 38.320 91.630 # SOURCE3 1 0.0000 + angle_coeff @angle:no-s6-o harmonic 39.210 107.430 # SOURCE3 6 1.5494 + angle_coeff @angle:n-s6-os harmonic 44.300 99.230 # SOURCE4 5 0.9794 + angle_coeff @angle:oh-s6-oh harmonic 46.090 100.340 # SOURCE3 6 0.0076 + angle_coeff @angle:oh-s6-os harmonic 47.130 96.620 # SOURCE4 26 0.6688 + angle_coeff @angle:oh-s6-p2 harmonic 37.140 109.670 # SOURCE3 2 0.0000 + angle_coeff @angle:o-s6-o harmonic 46.660 119.730 # SOURCE4 324 2.0530 + angle_coeff @angle:o-s6-oh harmonic 46.380 108.210 # SOURCE3 18 0.7437 + angle_coeff @angle:o-s6-os harmonic 46.660 107.840 # SOURCE3 12 0.7025 + angle_coeff @angle:o-s6-p2 harmonic 37.890 106.610 # SOURCE3 1 + angle_coeff @angle:o-s6-p3 harmonic 39.630 107.070 # SOURCE3 22 1.0550 + angle_coeff @angle:o-s6-p4 harmonic 36.540 105.670 # SOURCE3 1 + angle_coeff @angle:o-s6-p5 harmonic 40.380 106.640 # SOURCE3 1 + angle_coeff @angle:o-s6-s4 harmonic 49.910 107.850 # SOURCE3 1 + angle_coeff @angle:o-s6-s harmonic 50.300 110.290 # SOURCE3 6 2.2405 + angle_coeff @angle:o-s6-s6 harmonic 50.330 106.070 # SOURCE3 1 + angle_coeff @angle:o-s6-sh harmonic 49.520 106.810 # SOURCE3 6 0.6292 + angle_coeff @angle:os-s6-os harmonic 46.800 98.700 # SOURCE3 1 0.0000 + angle_coeff @angle:o-s6-ss harmonic 49.150 107.430 # SOURCE3 10 1.1423 + angle_coeff @angle:p3-s6-p3 harmonic 37.080 110.170 # SOURCE3 4 5.3678 + angle_coeff @angle:p5-s6-p5 harmonic 38.770 104.490 # SOURCE3 1 + angle_coeff @angle:s4-s6-s4 harmonic 61.650 101.990 # SOURCE3 1 + angle_coeff @angle:s4-s6-s6 harmonic 65.560 90.170 # SOURCE3 1 + angle_coeff @angle:s6-s6-s6 harmonic 61.260 103.290 # SOURCE3 1 + angle_coeff @angle:sh-s6-sh harmonic 59.550 106.430 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-s6-ss harmonic 60.490 102.640 # SOURCE3 1 + angle_coeff @angle:s-s6-s harmonic 60.770 109.340 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-s6-ss harmonic 60.590 101.820 # SOURCE3 1 0.0000 + angle_coeff @angle:br-sh-hs harmonic 27.240 95.640 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-sh-hs harmonic 30.170 95.990 # calculated_based_on_C#C-SH 0 + angle_coeff @angle:c2-sh-hs harmonic 28.660 97.080 # SOURCE4 5 0.3132 + angle_coeff @angle:c3-sh-hs harmonic 28.120 96.600 # SOURCE3 12 0.8009 + angle_coeff @angle:ca-sh-hs harmonic 28.980 94.840 # SOURCE4 13 0.4130 + angle_coeff @angle:cc-sh-hs harmonic 29.040 95.380 # SOURCE4 8 1.1410 + angle_coeff @angle:c-sh-hs harmonic 28.760 96.070 # SOURCE3 6 1.1164 + angle_coeff @angle:f-sh-hs harmonic 30.090 96.500 # SOURCE3 1 0.0000 + angle_coeff @angle:hs-sh-hs harmonic 23.430 93.720 # SOURCE3 3 0.4777 + angle_coeff @angle:hs-sh-i harmonic 23.210 96.440 # SOURCE3 1 0.0000 + angle_coeff @angle:hs-sh-n1 harmonic 32.340 93.510 # HF/6-31G* 1 + angle_coeff @angle:hs-sh-n2 harmonic 30.110 95.820 # SOURCE3 5 3.1495 + angle_coeff @angle:hs-sh-n harmonic 30.290 95.590 # SOURCE3 4 3.9065 + angle_coeff @angle:hs-sh-n3 harmonic 30.070 95.980 # SOURCE3 3 1.1735 + angle_coeff @angle:hs-sh-n4 harmonic 29.500 93.130 # SOURCE3 3 0.1675 + angle_coeff @angle:hs-sh-na harmonic 30.110 97.380 # SOURCE3 9 1.0223 + angle_coeff @angle:hs-sh-nh harmonic 29.730 101.110 # SOURCE3 1 0.0000 + angle_coeff @angle:hs-sh-no harmonic 29.630 92.930 # SOURCE3 1 0.0000 + angle_coeff @angle:hs-sh-o harmonic 30.170 109.230 # SOURCE3 2 0.0068 + angle_coeff @angle:hs-sh-oh harmonic 30.500 98.640 # SOURCE3 2 0.0605 + angle_coeff @angle:hs-sh-os harmonic 30.880 98.150 # SOURCE3 3 0.1661 + angle_coeff @angle:hs-sh-p2 harmonic 27.940 99.120 # SOURCE3 10 5.4110 + angle_coeff @angle:hs-sh-p3 harmonic 26.260 95.810 # SOURCE3 3 0.4396 + angle_coeff @angle:hs-sh-p4 harmonic 26.700 94.220 # SOURCE3 4 0.7605 + angle_coeff @angle:hs-sh-p5 harmonic 27.090 94.520 # SOURCE3 3 0.5589 + angle_coeff @angle:hs-sh-s harmonic 32.420 102.870 # SOURCE3 2 0.0000 + angle_coeff @angle:hs-sh-s4 harmonic 33.290 92.160 # SOURCE3 3 1.6519 + angle_coeff @angle:hs-sh-s6 harmonic 33.980 93.830 # SOURCE3 3 1.2561 + angle_coeff @angle:hs-sh-sh harmonic 33.890 99.070 # SOURCE3 2 0.0000 + angle_coeff @angle:hs-sh-ss harmonic 33.730 99.170 # SOURCE3 3 0.2457 + angle_coeff @angle:br-ss-br harmonic 41.920 102.920 # SOURCE3 1 0.0000 + angle_coeff @angle:br-ss-c3 harmonic 39.460 99.030 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-ss-c1 harmonic 41.480 98.300 # SOURCE2 1 0.0000 + angle_coeff @angle:c1-ss-c3 harmonic 39.350 99.900 # SOURCE2 1 0.0000 + angle_coeff @angle:c2-ss-c2 harmonic 39.870 99.560 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-ss-c3 harmonic 38.710 100.370 # SOURCE4 100 2.3280 + angle_coeff @angle:c2-ss-cy harmonic 40.860 88.610 # SOURCE4 27 0.4481 + angle_coeff @angle:c2-ss-n2 harmonic 40.330 106.760 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-ss-na harmonic 40.680 100.510 # SOURCE3 6 6.9702 + angle_coeff @angle:c2-ss-os harmonic 43.660 89.760 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-ss-ss harmonic 51.300 92.260 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-ss-c3 harmonic 37.940 99.920 # SOURCE3 14 2.0723 + angle_coeff @angle:c3-ss-ca harmonic 38.040 102.120 # SOURCE4 161 1.3084 + angle_coeff @angle:c3-ss-cc harmonic 38.610 100.850 # SOURCE4 74 1.3149 + angle_coeff @angle:c3-ss-cd harmonic 38.730 100.210 # SOURCE4 13 1.3340 + angle_coeff @angle:c3-ss-cl harmonic 37.940 99.400 # SOURCE2 1 0.0000 + angle_coeff @angle:c3-ss-cy harmonic 38.750 94.320 # SOURCE4 62 0.3646 + angle_coeff @angle:c3-ss-f harmonic 39.670 97.490 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-ss-i harmonic 35.060 100.000 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-ss-n1 harmonic 41.250 98.440 # HF/6-31G* 1 + angle_coeff @angle:c3-ss-n2 harmonic 41.260 96.420 # SOURCE3 5 1.3604 + angle_coeff @angle:c3-ss-n3 harmonic 40.110 98.830 # SOURCE3 3 0.2909 + angle_coeff @angle:c3-ss-n harmonic 39.860 100.300 # SOURCE3 4 0.6579 + angle_coeff @angle:c3-ss-n4 harmonic 39.380 97.790 # SOURCE3 3 0.2002 + angle_coeff @angle:c3-ss-na harmonic 39.740 100.140 # SOURCE3 12 1.7415 + angle_coeff @angle:c3-ss-nh harmonic 39.890 100.630 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-ss-no harmonic 39.050 98.620 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-ss-o harmonic 40.460 106.600 # SOURCE3 2 1.6714 + angle_coeff @angle:c3-ss-oh harmonic 40.850 98.280 # SOURCE3 2 1.4326 + angle_coeff @angle:c3-ss-os harmonic 40.650 98.210 # SOURCE3 4 1.7097 + angle_coeff @angle:c3-ss-p2 harmonic 39.660 98.410 # SOURCE3 8 0.9454 + angle_coeff @angle:c3-ss-p3 harmonic 37.720 98.700 # SOURCE3 3 0.0356 + angle_coeff @angle:c3-ss-p4 harmonic 38.030 98.160 # SOURCE3 4 0.1361 + angle_coeff @angle:c3-ss-p5 harmonic 37.500 100.220 # SOURCE4 23 1.1410 + angle_coeff @angle:c3-ss-s4 harmonic 47.600 96.370 # SOURCE3 3 0.0202 + angle_coeff @angle:c3-ss-s harmonic 47.470 101.900 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-ss-s6 harmonic 48.260 96.760 # SOURCE3 3 1.5680 + angle_coeff @angle:c3-ss-sh harmonic 47.800 101.930 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-ss-ss harmonic 47.780 103.100 # SOURCE4 70 1.3377 + angle_coeff @angle:ca-ss-ca harmonic 39.270 98.710 # SOURCE4 97 1.2321 + angle_coeff @angle:ca-ss-cc harmonic 41.730 89.010 # SOURCE4 88 1.2324 + angle_coeff @angle:ca-ss-cd harmonic 41.420 90.360 # SOURCE4 46 0.9833 + angle_coeff @angle:ca-ss-cl harmonic 37.980 101.050 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-ss-n harmonic 41.150 97.160 # SOURCE3 1 + angle_coeff @angle:ca-ss-na harmonic 40.520 99.320 # SOURCE3 1 + angle_coeff @angle:ca-ss-nc harmonic 43.300 94.760 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-ss-nd harmonic 43.300 94.760 # SOURCE3 1 same_as_ca-ss-nc + angle_coeff @angle:ca-ss-ss harmonic 47.820 104.900 # SOURCE4 19 0.8743 + angle_coeff @angle:c-ss-c2 harmonic 41.060 92.430 # SOURCE3 1 0.0000 + angle_coeff @angle:c-ss-c3 harmonic 38.470 100.290 # SOURCE3 5 2.2127 + angle_coeff @angle:c-ss-c harmonic 38.920 101.400 # SOURCE3 1 0.0000 + angle_coeff @angle:c-ss-cc harmonic 41.050 92.430 # SOURCE4 14 2.3600 + angle_coeff @angle:cc-ss-cc harmonic 41.930 89.910 # SOURCE3 11 2.2164 + angle_coeff @angle:cc-ss-cd harmonic 41.970 89.740 # SOURCE4 49 0.7509 + angle_coeff @angle:cc-ss-n harmonic 41.560 97.160 # SOURCE3 1 same_as_cd-ss-n + angle_coeff @angle:cc-ss-na harmonic 40.910 99.330 # SOURCE3 18 same_as_cd-ss-na + angle_coeff @angle:cc-ss-nc harmonic 44.100 93.610 # SOURCE4 10 0.8252 + angle_coeff @angle:cc-ss-os harmonic 41.600 98.810 # SOURCE3 2 2.1583 + angle_coeff @angle:cc-ss-ss harmonic 48.670 102.460 # SOURCE3 2 0.0000 + angle_coeff @angle:cd-ss-cd harmonic 41.930 89.910 # SOURCE3 11 2.2164 + angle_coeff @angle:cd-ss-n harmonic 41.560 97.160 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-ss-na harmonic 40.910 99.330 # SOURCE3 18 2.5847 + angle_coeff @angle:cd-ss-nd harmonic 43.630 95.660 # SOURCE3 3 0.0000 + angle_coeff @angle:cd-ss-os harmonic 41.600 98.810 # SOURCE3 2 same_as_cc-ss-os + angle_coeff @angle:cd-ss-ss harmonic 50.980 93.360 # SOURCE4 11 0.3795 + angle_coeff @angle:cl-ss-cl harmonic 37.900 103.370 # SOURCE3 1 0.0000 + angle_coeff @angle:cx-ss-cx harmonic 54.740 48.300 # SOURCE2 1 0.0000 + angle_coeff @angle:f-ss-f harmonic 41.410 98.300 # SOURCE2 1 0.0000 + angle_coeff @angle:f-ss-ss harmonic 47.400 108.300 # SOURCE2 1 0.0000 + angle_coeff @angle:i-ss-i harmonic 36.380 106.290 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-ss-n1 harmonic 45.720 96.960 # HF/6-31G* 1 + angle_coeff @angle:n2-ss-n2 harmonic 44.500 96.750 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-ss-n3 harmonic 41.610 102.340 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-ss-n4 harmonic 39.760 101.190 # SOURCE3 1 0.0000 + angle_coeff @angle:na-ss-na harmonic 41.250 102.810 # SOURCE3 1 0.0000 + angle_coeff @angle:nc-ss-nc harmonic 46.990 97.750 # SOURCE4 8 0.3345 + angle_coeff @angle:nd-ss-nd harmonic 46.580 99.500 # SOURCE2 1 same_as_nc-ss-nc + angle_coeff @angle:nh-ss-nh harmonic 40.860 107.890 # SOURCE3 1 0.0000 + angle_coeff @angle:n-ss-n harmonic 41.570 103.100 # SOURCE3 1 0.0000 + angle_coeff @angle:no-ss-no harmonic 38.430 106.430 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-ss-oh harmonic 42.690 104.250 # SOURCE3 1 0.0000 + angle_coeff @angle:o-ss-o harmonic 43.680 119.300 # SOURCE2 1 0.0000 + angle_coeff @angle:o-ss-p5 harmonic 38.880 106.410 # SOURCE3 1 0.0000 + angle_coeff @angle:o-ss-s6 harmonic 49.380 105.390 # SOURCE3 1 + angle_coeff @angle:os-ss-os harmonic 42.400 102.990 # SOURCE3 1 0.0000 + angle_coeff @angle:o-ss-ss harmonic 49.130 112.700 # SOURCE2 1 0.0000 + angle_coeff @angle:p2-ss-p2 harmonic 41.220 99.520 # SOURCE3 1 0.0000 + angle_coeff @angle:p3-ss-p3 harmonic 37.800 101.670 # SOURCE3 1 + angle_coeff @angle:p5-ss-p5 harmonic 40.330 89.830 # SOURCE3 1 0.0000 + angle_coeff @angle:s4-ss-s4 harmonic 60.990 96.080 # SOURCE3 1 0.0000 + angle_coeff @angle:s4-ss-s6 harmonic 60.060 101.260 # SOURCE3 1 + angle_coeff @angle:s6-ss-s6 harmonic 60.590 101.810 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-ss-sh harmonic 60.410 107.540 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-ss-ss harmonic 60.950 106.530 # SOURCE3 1 + angle_coeff @angle:s-ss-s harmonic 57.790 115.040 # SOURCE3 1 + angle_coeff @angle:ss-ss-ss harmonic 60.570 108.760 # SOURCE4 8 0.2385 + angle_coeff @angle:c3-sx-ca harmonic 38.700 96.410 # SOURCE4 13 0.3130 + angle_coeff @angle:c3-sx-cc harmonic 39.120 95.110 # SOURCE4 17 0.6557 + angle_coeff @angle:c3-sx-ce harmonic 39.300 94.950 # SOURCE3 3 0.0007 + angle_coeff @angle:c3-sx-cf harmonic 39.300 94.950 # SOURCE3 3 same_as_c3-sx-ce + angle_coeff @angle:c3-sx-ne harmonic 40.880 90.060 # SOURCE3 5 1.9627 + angle_coeff @angle:c3-sx-nf harmonic 40.880 90.060 # SOURCE3 5 same_as_c3-sx-ne + angle_coeff @angle:c3-sx-o harmonic 40.630 107.880 # SOURCE3 30 0.8721 + angle_coeff @angle:c3-sx-pe harmonic 38.060 94.320 # SOURCE3 7 0.5547 + angle_coeff @angle:c3-sx-pf harmonic 38.060 94.320 # SOURCE3 7 same_as_c3-sx-pe + angle_coeff @angle:c3-sx-px harmonic 36.710 96.460 # SOURCE3 3 1.3351 + angle_coeff @angle:c3-sx-py harmonic 36.650 95.670 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-sx-sx harmonic 45.310 91.470 # SOURCE3 4 1.9919 + angle_coeff @angle:c3-sx-sy harmonic 46.490 95.470 # SOURCE3 3 2.8422 + angle_coeff @angle:ca-sx-ca harmonic 38.770 95.210 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-sx-o harmonic 40.550 106.890 # SOURCE4 25 0.5562 + angle_coeff @angle:c-sx-c3 harmonic 38.800 92.710 # SOURCE3 3 0.3095 + angle_coeff @angle:c-sx-c harmonic 39.310 86.850 # SOURCE3 1 0.0000 + angle_coeff @angle:cc-sx-o harmonic 41.250 104.490 # SOURCE4 17 1.7759 + angle_coeff @angle:ce-sx-ce harmonic 39.430 94.960 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-sx-o harmonic 40.910 107.470 # SOURCE3 5 0.3128 + angle_coeff @angle:cf-sx-cf harmonic 39.430 94.960 # SOURCE3 1 same_as_ce-sx-ce + angle_coeff @angle:cf-sx-o harmonic 40.910 107.470 # SOURCE3 5 same_as_ce-sx-o + angle_coeff @angle:c-sx-o harmonic 39.710 106.170 # SOURCE3 5 0.9477 + angle_coeff @angle:ne-sx-ne harmonic 41.530 90.170 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-sx-o harmonic 40.900 109.200 # SOURCE3 7 1.4542 + angle_coeff @angle:nf-sx-nf harmonic 41.530 90.170 # SOURCE3 1 same_as_ne-sx-ne + angle_coeff @angle:nf-sx-o harmonic 40.900 109.200 # SOURCE3 7 same_as_ne-sx-o + angle_coeff @angle:o-sx-pe harmonic 38.070 106.430 # SOURCE3 9 2.8345 + angle_coeff @angle:o-sx-pf harmonic 38.070 106.430 # SOURCE3 9 same_as_o-sx-pe + angle_coeff @angle:o-sx-px harmonic 37.160 104.770 # SOURCE3 3 1.9810 + angle_coeff @angle:o-sx-py harmonic 36.140 109.130 # SOURCE3 7 5.6840 + angle_coeff @angle:o-sx-sx harmonic 44.100 104.650 # SOURCE3 6 3.0524 + angle_coeff @angle:o-sx-sy harmonic 47.070 103.410 # SOURCE3 5 0.9618 + angle_coeff @angle:pe-sx-pe harmonic 38.750 92.620 # SOURCE3 1 0.0000 + angle_coeff @angle:pf-sx-pf harmonic 38.750 92.620 # SOURCE3 1 same_as_pe-sx-pe + angle_coeff @angle:py-sx-py harmonic 43.010 69.230 # SOURCE3 3 17.4143 + angle_coeff @angle:sx-sx-sx harmonic 58.780 84.900 # SOURCE3 1 0.0000 + angle_coeff @angle:sy-sx-sy harmonic 59.380 93.520 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-sy-ca harmonic 38.000 103.860 # SOURCE4 54 0.3180 + angle_coeff @angle:c3-sy-cc harmonic 38.280 102.190 # SOURCE4 12 1.5324 + angle_coeff @angle:c3-sy-ce harmonic 38.030 103.810 # SOURCE3 3 0.3368 + angle_coeff @angle:c3-sy-cf harmonic 38.030 103.810 # SOURCE3 3 same_as_c3-sy-ce + angle_coeff @angle:c3-sy-ne harmonic 39.420 103.120 # SOURCE3 5 4.1882 + angle_coeff @angle:c3-sy-nf harmonic 39.420 103.120 # SOURCE3 5 same_as_c3-sy-ne + angle_coeff @angle:c3-sy-o harmonic 41.280 108.480 # SOURCE3 62 0.8576 + angle_coeff @angle:c3-sy-pe harmonic 35.490 106.030 # SOURCE3 6 2.6117 + angle_coeff @angle:c3-sy-pf harmonic 35.490 106.030 # SOURCE3 6 same_as_c3-sy-pe + angle_coeff @angle:c3-sy-px harmonic 35.450 103.620 # SOURCE3 3 0.7078 + angle_coeff @angle:c3-sy-py harmonic 36.330 103.390 # SOURCE3 3 0.4563 + angle_coeff @angle:c3-sy-sx harmonic 44.560 104.640 # SOURCE3 3 4.6276 + angle_coeff @angle:c3-sy-sy harmonic 45.480 100.780 # SOURCE3 4 1.1633 + angle_coeff @angle:ca-sy-ca harmonic 37.950 104.040 # SOURCE4 25 2.0762 + angle_coeff @angle:ca-sy-cc harmonic 37.720 105.090 # SOURCE4 5 0.3628 + angle_coeff @angle:ca-sy-n3 harmonic 40.110 102.480 # SOURCE4 180 1.0802 + angle_coeff @angle:ca-sy-n harmonic 39.350 105.450 # SOURCE4 51 1.1497 + angle_coeff @angle:ca-sy-ne harmonic 39.330 103.470 # SOURCE4 11 1.6071 + angle_coeff @angle:ca-sy-nh harmonic 39.330 105.590 # SOURCE4 78 1.5805 + angle_coeff @angle:ca-sy-o harmonic 41.200 108.730 # SOURCE3 26 1.2638 + angle_coeff @angle:ca-sy-oh harmonic 41.070 101.250 # SOURCE4 23 0.9100 + angle_coeff @angle:ca-sy-os harmonic 42.320 92.980 # SOURCE3 1 0.0000 + angle_coeff @angle:c-sy-c3 harmonic 37.600 101.250 # SOURCE3 3 1.1850 + angle_coeff @angle:c-sy-c harmonic 37.060 99.810 # SOURCE3 1 0.0000 + angle_coeff @angle:cc-sy-n3 harmonic 40.090 102.390 # SOURCE4 17 0.6395 + angle_coeff @angle:cc-sy-o harmonic 41.420 107.270 # SOURCE4 62 0.9782 + angle_coeff @angle:cd-sy-n3 harmonic 40.140 102.730 # SOURCE4 13 0.5722 + angle_coeff @angle:cd-sy-nh harmonic 41.070 97.200 # SOURCE4 6 0.2429 + angle_coeff @angle:cd-sy-o harmonic 41.360 108.420 # SOURCE4 38 0.6229 + angle_coeff @angle:ce-sy-ce harmonic 38.220 102.780 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-sy-o harmonic 41.510 107.250 # SOURCE3 10 0.5477 + angle_coeff @angle:cf-sy-cf harmonic 38.220 102.780 # SOURCE3 1 same_as_ce-sy-ce + angle_coeff @angle:cf-sy-o harmonic 41.510 107.250 # SOURCE3 10 same_as_ce-sy-o + angle_coeff @angle:c-sy-o harmonic 40.090 107.230 # SOURCE3 10 0.8425 + angle_coeff @angle:f-sy-o harmonic 45.090 105.600 # SOURCE4 7 0.2000 + angle_coeff @angle:n2-sy-o harmonic 43.410 123.530 # SOURCE4 6 1.2388 + angle_coeff @angle:n3-sy-ne harmonic 41.520 102.400 # SOURCE4 5 1.3390 + angle_coeff @angle:n3-sy-o harmonic 44.080 107.110 # SOURCE4 375 1.1257 + angle_coeff @angle:na-sy-na harmonic 42.390 98.040 # SOURCE3 1 + angle_coeff @angle:nc-sy-nc harmonic 47.080 98.040 # SOURCE3 2 + angle_coeff @angle:nd-sy-nd harmonic 47.080 98.040 # SOURCE3 2 + angle_coeff @angle:ne-sy-ne harmonic 41.660 98.620 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-sy-o harmonic 43.100 107.060 # SOURCE3 14 2.2705 + angle_coeff @angle:nf-sy-nf harmonic 41.660 98.620 # SOURCE3 1 same_as_ne-sy-ne + angle_coeff @angle:nf-sy-o harmonic 43.100 107.060 # SOURCE3 14 same_as_ne-sy-o + angle_coeff @angle:nh-sy-o harmonic 43.910 106.380 # SOURCE4 123 1.6517 + angle_coeff @angle:n-sy-o harmonic 43.660 107.500 # SOURCE4 61 1.8720 + angle_coeff @angle:o-sy-o harmonic 45.300 121.880 # SOURCE3 46 0.9495 + angle_coeff @angle:o-sy-oh harmonic 45.210 106.930 # SOURCE3 8 0.7424 + angle_coeff @angle:o-sy-os harmonic 44.040 108.310 # SOURCE4 7 0.1222 + angle_coeff @angle:o-sy-pe harmonic 37.280 106.900 # SOURCE3 12 1.4524 + angle_coeff @angle:o-sy-pf harmonic 37.280 106.900 # SOURCE3 12 same_as_o-sy-pe + angle_coeff @angle:o-sy-px harmonic 36.810 106.170 # SOURCE3 6 0.7059 + angle_coeff @angle:o-sy-py harmonic 37.840 106.670 # SOURCE3 10 0.6478 + angle_coeff @angle:o-sy-sx harmonic 46.420 106.330 # SOURCE3 10 2.0456 + angle_coeff @angle:o-sy-sy harmonic 46.560 106.190 # SOURCE3 12 0.1754 + angle_coeff @angle:py-sy-py harmonic 36.250 104.490 # SOURCE3 1 0.0000 + angle_coeff @angle:sx-sy-sx harmonic 56.860 101.990 # SOURCE3 1 0.0000 + angle_coeff @angle:sy-sy-sy harmonic 56.630 103.290 # SOURCE3 1 0.0000 + } # (end of angle_coeffs) + + write_once("Data Angles By Type") { + @angle:hw-ow-hw @atom:hw @atom:ow @atom:hw + @angle:hw-hw-ow @atom:hw @atom:hw @atom:ow + @angle:br-c1-br @atom:br @atom:c1 @atom:br + @angle:br-c1-c1 @atom:br @atom:c1 @atom:c1 + @angle:c1-c1-c1 @atom:c1 @atom:c1 @atom:c1 + @angle:c1-c1-c2 @atom:c1 @atom:c1 @atom:c2 + @angle:c1-c1-c3 @atom:c1 @atom:c1 @atom:c3 + @angle:c1-c1-ca @atom:c1 @atom:c1 @atom:ca + @angle:c1-c1-cl @atom:c1 @atom:c1 @atom:cl + @angle:c1-c1-f @atom:c1 @atom:c1 @atom:f + @angle:c1-c1-ha @atom:c1 @atom:c1 @atom:ha + @angle:c1-c1-hc @atom:c1 @atom:c1 @atom:hc + @angle:c1-c1-i @atom:c1 @atom:c1 @atom:i + @angle:c1-c1-n1 @atom:c1 @atom:c1 @atom:n1 + @angle:c1-c1-n2 @atom:c1 @atom:c1 @atom:n2 + @angle:c1-c1-n3 @atom:c1 @atom:c1 @atom:n3 + @angle:c1-c1-n4 @atom:c1 @atom:c1 @atom:n4 + @angle:c1-c1-n @atom:c1 @atom:c1 @atom:n + @angle:c1-c1-na @atom:c1 @atom:c1 @atom:na + @angle:c1-c1-nh @atom:c1 @atom:c1 @atom:nh + @angle:c1-c1-no @atom:c1 @atom:c1 @atom:no + @angle:c1-c1-o @atom:c1 @atom:c1 @atom:o + @angle:c1-c1-oh @atom:c1 @atom:c1 @atom:oh + @angle:c1-c1-os @atom:c1 @atom:c1 @atom:os + @angle:c1-c1-p2 @atom:c1 @atom:c1 @atom:p2 + @angle:c1-c1-p3 @atom:c1 @atom:c1 @atom:p3 + @angle:c1-c1-p4 @atom:c1 @atom:c1 @atom:p4 + @angle:c1-c1-p5 @atom:c1 @atom:c1 @atom:p5 + @angle:c1-c1-s4 @atom:c1 @atom:c1 @atom:s4 + @angle:c1-c1-s6 @atom:c1 @atom:c1 @atom:s6 + @angle:c1-c1-s @atom:c1 @atom:c1 @atom:s + @angle:c1-c1-sh @atom:c1 @atom:c1 @atom:sh + @angle:c1-c1-ss @atom:c1 @atom:c1 @atom:ss + @angle:c2-c1-c2 @atom:c2 @atom:c1 @atom:c2 + @angle:c2-c1-ce @atom:c2 @atom:c1 @atom:ce + @angle:c2-c1-n1 @atom:c2 @atom:c1 @atom:n1 + @angle:c2-c1-o @atom:c2 @atom:c1 @atom:o + @angle:c2-c1-s2 @atom:c2 @atom:c1 @atom:s2 + @angle:c3-c1-c3 @atom:c3 @atom:c1 @atom:c3 + @angle:c3-c1-cg @atom:c3 @atom:c1 @atom:cg + @angle:c3-c1-n1 @atom:c3 @atom:c1 @atom:n1 + @angle:ca-c1-ca @atom:ca @atom:c1 @atom:ca + @angle:c-c1-c1 @atom:c @atom:c1 @atom:c1 + @angle:cg-c1-ha @atom:cg @atom:c1 @atom:ha + @angle:ch-c1-ha @atom:ch @atom:c1 @atom:ha + @angle:cl-c1-cl @atom:cl @atom:c1 @atom:cl + @angle:f-c1-f @atom:f @atom:c1 @atom:f + @angle:i-c1-i @atom:i @atom:c1 @atom:i + @angle:n1-c1-n1 @atom:n1 @atom:c1 @atom:n1 + @angle:n1-c1-n3 @atom:n1 @atom:c1 @atom:n3 + @angle:n1-c1-nh @atom:n1 @atom:c1 @atom:nh + @angle:n1-c1-os @atom:n1 @atom:c1 @atom:os + @angle:n1-c1-p3 @atom:n1 @atom:c1 @atom:p3 + @angle:n1-c1-ss @atom:n1 @atom:c1 @atom:ss + @angle:n2-c1-n2 @atom:n2 @atom:c1 @atom:n2 + @angle:n2-c1-o @atom:n2 @atom:c1 @atom:o + @angle:n2-c1-s @atom:n2 @atom:c1 @atom:s + @angle:n3-c1-n3 @atom:n3 @atom:c1 @atom:n3 + @angle:n4-c1-n4 @atom:n4 @atom:c1 @atom:n4 + @angle:na-c1-na @atom:na @atom:c1 @atom:na + @angle:ne-c1-o @atom:ne @atom:c1 @atom:o + @angle:ne-c1-s @atom:ne @atom:c1 @atom:s + @angle:nf-c1-o @atom:nf @atom:c1 @atom:o + @angle:nh-c1-nh @atom:nh @atom:c1 @atom:nh + @angle:n-c1-n @atom:n @atom:c1 @atom:n + @angle:no-c1-no @atom:no @atom:c1 @atom:no + @angle:oh-c1-oh @atom:oh @atom:c1 @atom:oh + @angle:o-c1-o @atom:o @atom:c1 @atom:o + @angle:os-c1-os @atom:os @atom:c1 @atom:os + @angle:p2-c1-p2 @atom:p2 @atom:c1 @atom:p2 + @angle:p3-c1-p3 @atom:p3 @atom:c1 @atom:p3 + @angle:p4-c1-p4 @atom:p4 @atom:c1 @atom:p4 + @angle:p5-c1-p5 @atom:p5 @atom:c1 @atom:p5 + @angle:s2-c1-s2 @atom:s2 @atom:c1 @atom:s2 + @angle:s4-c1-s4 @atom:s4 @atom:c1 @atom:s4 + @angle:s6-c1-s6 @atom:s6 @atom:c1 @atom:s6 + @angle:sh-c1-sh @atom:sh @atom:c1 @atom:sh + @angle:s-c1-s @atom:s @atom:c1 @atom:s + @angle:ss-c1-ss @atom:ss @atom:c1 @atom:ss + @angle:br-c2-br @atom:br @atom:c2 @atom:br + @angle:br-c2-c2 @atom:br @atom:c2 @atom:c2 + @angle:br-c2-c3 @atom:br @atom:c2 @atom:c3 + @angle:br-c2-ce @atom:br @atom:c2 @atom:ce + @angle:br-c2-h4 @atom:br @atom:c2 @atom:h4 + @angle:br-c2-ha @atom:br @atom:c2 @atom:ha + @angle:c1-c2-c1 @atom:c1 @atom:c2 @atom:c1 + @angle:c1-c2-c2 @atom:c1 @atom:c2 @atom:c2 + @angle:c1-c2-c3 @atom:c1 @atom:c2 @atom:c3 + @angle:c1-c2-f @atom:c1 @atom:c2 @atom:f + @angle:c1-c2-ha @atom:c1 @atom:c2 @atom:ha + @angle:c2-c2-c2 @atom:c2 @atom:c2 @atom:c2 + @angle:c2-c2-c3 @atom:c2 @atom:c2 @atom:c3 + @angle:c2-c2-ca @atom:c2 @atom:c2 @atom:ca + @angle:c2-c2-cc @atom:c2 @atom:c2 @atom:cc + @angle:c2-c2-cd @atom:c2 @atom:c2 @atom:cd + @angle:c2-c2-cl @atom:c2 @atom:c2 @atom:cl + @angle:c2-c2-cx @atom:c2 @atom:c2 @atom:cx + @angle:c2-c2-cy 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@angle:c3-sx-o @atom:c3 @atom:sx @atom:o + @angle:c3-sx-pe @atom:c3 @atom:sx @atom:pe + @angle:c3-sx-pf @atom:c3 @atom:sx @atom:pf + @angle:c3-sx-px @atom:c3 @atom:sx @atom:px + @angle:c3-sx-py @atom:c3 @atom:sx @atom:py + @angle:c3-sx-sx @atom:c3 @atom:sx @atom:sx + @angle:c3-sx-sy @atom:c3 @atom:sx @atom:sy + @angle:ca-sx-ca @atom:ca @atom:sx @atom:ca + @angle:ca-sx-o @atom:ca @atom:sx @atom:o + @angle:c-sx-c3 @atom:c @atom:sx @atom:c3 + @angle:c-sx-c @atom:c @atom:sx @atom:c + @angle:cc-sx-o @atom:cc @atom:sx @atom:o + @angle:ce-sx-ce @atom:ce @atom:sx @atom:ce + @angle:ce-sx-o @atom:ce @atom:sx @atom:o + @angle:cf-sx-cf @atom:cf @atom:sx @atom:cf + @angle:cf-sx-o @atom:cf @atom:sx @atom:o + @angle:c-sx-o @atom:c @atom:sx @atom:o + @angle:ne-sx-ne @atom:ne @atom:sx @atom:ne + @angle:ne-sx-o @atom:ne @atom:sx @atom:o + @angle:nf-sx-nf @atom:nf @atom:sx @atom:nf + @angle:nf-sx-o @atom:nf @atom:sx @atom:o + @angle:o-sx-pe @atom:o @atom:sx @atom:pe + @angle:o-sx-pf @atom:o @atom:sx @atom:pf + @angle:o-sx-px @atom:o @atom:sx @atom:px + @angle:o-sx-py @atom:o @atom:sx @atom:py + @angle:o-sx-sx @atom:o @atom:sx @atom:sx + @angle:o-sx-sy @atom:o @atom:sx @atom:sy + @angle:pe-sx-pe @atom:pe @atom:sx @atom:pe + @angle:pf-sx-pf @atom:pf @atom:sx @atom:pf + @angle:py-sx-py @atom:py @atom:sx @atom:py + @angle:sx-sx-sx @atom:sx @atom:sx @atom:sx + @angle:sy-sx-sy @atom:sy @atom:sx @atom:sy + @angle:c3-sy-ca @atom:c3 @atom:sy @atom:ca + @angle:c3-sy-cc @atom:c3 @atom:sy @atom:cc + @angle:c3-sy-ce @atom:c3 @atom:sy @atom:ce + @angle:c3-sy-cf @atom:c3 @atom:sy @atom:cf + @angle:c3-sy-ne @atom:c3 @atom:sy @atom:ne + @angle:c3-sy-nf @atom:c3 @atom:sy @atom:nf + @angle:c3-sy-o @atom:c3 @atom:sy @atom:o + @angle:c3-sy-pe @atom:c3 @atom:sy @atom:pe + @angle:c3-sy-pf @atom:c3 @atom:sy @atom:pf + @angle:c3-sy-px @atom:c3 @atom:sy @atom:px + @angle:c3-sy-py @atom:c3 @atom:sy @atom:py + @angle:c3-sy-sx @atom:c3 @atom:sy @atom:sx + @angle:c3-sy-sy @atom:c3 @atom:sy @atom:sy + @angle:ca-sy-ca @atom:ca @atom:sy @atom:ca + @angle:ca-sy-cc @atom:ca @atom:sy @atom:cc + @angle:ca-sy-n3 @atom:ca @atom:sy @atom:n3 + @angle:ca-sy-n @atom:ca @atom:sy @atom:n + @angle:ca-sy-ne @atom:ca @atom:sy @atom:ne + @angle:ca-sy-nh @atom:ca @atom:sy @atom:nh + @angle:ca-sy-o @atom:ca @atom:sy @atom:o + @angle:ca-sy-oh @atom:ca @atom:sy @atom:oh + @angle:ca-sy-os @atom:ca @atom:sy @atom:os + @angle:c-sy-c3 @atom:c @atom:sy @atom:c3 + @angle:c-sy-c @atom:c @atom:sy @atom:c + @angle:cc-sy-n3 @atom:cc @atom:sy @atom:n3 + @angle:cc-sy-o @atom:cc @atom:sy @atom:o + @angle:cd-sy-n3 @atom:cd @atom:sy @atom:n3 + @angle:cd-sy-nh @atom:cd @atom:sy @atom:nh + @angle:cd-sy-o @atom:cd @atom:sy @atom:o + @angle:ce-sy-ce @atom:ce @atom:sy @atom:ce + @angle:ce-sy-o @atom:ce @atom:sy @atom:o + @angle:cf-sy-cf @atom:cf @atom:sy @atom:cf + @angle:cf-sy-o @atom:cf @atom:sy @atom:o + @angle:c-sy-o @atom:c @atom:sy @atom:o + @angle:f-sy-o @atom:f @atom:sy @atom:o + @angle:n2-sy-o @atom:n2 @atom:sy @atom:o + @angle:n3-sy-ne @atom:n3 @atom:sy @atom:ne + @angle:n3-sy-o @atom:n3 @atom:sy @atom:o + @angle:na-sy-na @atom:na @atom:sy @atom:na + @angle:nc-sy-nc @atom:nc @atom:sy @atom:nc + @angle:nd-sy-nd @atom:nd @atom:sy @atom:nd + @angle:ne-sy-ne @atom:ne @atom:sy @atom:ne + @angle:ne-sy-o @atom:ne @atom:sy @atom:o + @angle:nf-sy-nf @atom:nf @atom:sy @atom:nf + @angle:nf-sy-o @atom:nf @atom:sy @atom:o + @angle:nh-sy-o @atom:nh @atom:sy @atom:o + @angle:n-sy-o @atom:n @atom:sy @atom:o + @angle:o-sy-o @atom:o @atom:sy @atom:o + @angle:o-sy-oh @atom:o @atom:sy @atom:oh + @angle:o-sy-os @atom:o @atom:sy @atom:os + @angle:o-sy-pe @atom:o @atom:sy @atom:pe + @angle:o-sy-pf @atom:o @atom:sy @atom:pf + @angle:o-sy-px @atom:o @atom:sy @atom:px + @angle:o-sy-py @atom:o @atom:sy @atom:py + @angle:o-sy-sx @atom:o @atom:sy @atom:sx + @angle:o-sy-sy @atom:o @atom:sy @atom:sy + @angle:py-sy-py @atom:py @atom:sy @atom:py + @angle:sx-sy-sx @atom:sx @atom:sy @atom:sx + @angle:sy-sy-sy @atom:sy @atom:sy @atom:sy + } # (end of Angles By Type) + + write_once("In Settings") { + dihedral_coeff @dihedral:X-c-c-X fourier 1 0.3 2 180.0 # + dihedral_coeff @dihedral:X-c-c1-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c-cg-X fourier 1 0.0 2 180.0 # same as X-c-c1-X + dihedral_coeff @dihedral:X-c-ch-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c-c2-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-cu-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-cv-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-ce-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-cf-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-c3-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230 + dihedral_coeff @dihedral:X-c-cx-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230 + dihedral_coeff @dihedral:X-c-cy-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230 + dihedral_coeff @dihedral:X-c-ca-X fourier 1 1.0 2 180.0 # optimized by Junmei Wang, Jan-2013 + dihedral_coeff @dihedral:X-c-cc-X fourier 1 2.875 2 180.0 # statistic value + dihedral_coeff @dihedral:X-c-cd-X fourier 1 2.875 2 180.0 # statistic value + dihedral_coeff @dihedral:X-c-n-X fourier 1 2.5 2 180.0 # AA,NMA (no c-n3, c-n4, c-nh) + dihedral_coeff @dihedral:X-c-n2-X fourier 1 4.15 2 180.0 # double bond, same as X-c2-n2-X + dihedral_coeff @dihedral:X-c-nc-X fourier 1 4.0 2 180.0 # same as X-C-NC-X + dihedral_coeff @dihedral:X-c-nd-X fourier 1 4.0 2 180.0 # same as X-C-NC-X + dihedral_coeff @dihedral:X-c-ne-X fourier 1 0.2 2 180.0 # single bond + dihedral_coeff @dihedral:X-c-nf-X fourier 1 0.2 2 180.0 # single bond + dihedral_coeff @dihedral:X-c-na-X fourier 2 1.45 2 180.0 0.35 4 180.0 # + dihedral_coeff @dihedral:X-c-no-X fourier 1 0.45 2 180.0 # + dihedral_coeff @dihedral:X-c-oh-X fourier 1 2.3 2 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:X-c-os-X fourier 1 2.7 2 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:X-c-p2-X fourier 1 6.65 2 180.0 # double bond, same as X-c2-p2-X + dihedral_coeff @dihedral:X-c-pc-X fourier 1 2.0 2 180.0 # estimated + dihedral_coeff @dihedral:X-c-pd-X fourier 1 2.0 2 180.0 # estimated + dihedral_coeff @dihedral:X-c-pe-X fourier 1 0.0 2 180.0 # single bond + dihedral_coeff @dihedral:X-c-pf-X fourier 1 0.0 2 180.0 # single bond + dihedral_coeff @dihedral:X-c-p3-X fourier 1 1.55 2 180.0 # + dihedral_coeff @dihedral:X-c-p4-X fourier 1 1.35 2 180.0 # + dihedral_coeff @dihedral:X-c-px-X fourier 1 1.35 2 180.0 # + dihedral_coeff @dihedral:X-c-p5-X fourier 1 1.0 2 0.0 # + dihedral_coeff @dihedral:X-c-py-X fourier 1 1.0 2 0.0 # + dihedral_coeff @dihedral:X-c-sh-X fourier 1 2.25 2 180.0 # + dihedral_coeff @dihedral:X-c-ss-X fourier 1 3.1 2 180.0 # + dihedral_coeff @dihedral:X-c-s4-X fourier 1 0.2 2 180.0 # + dihedral_coeff @dihedral:X-c-sx-X fourier 1 0.2 2 180.0 # + dihedral_coeff @dihedral:X-c-s6-X fourier 1 0.5 2 0.0 # + dihedral_coeff @dihedral:X-c-sy-X fourier 1 0.5 2 0.0 # + dihedral_coeff @dihedral:X-c1-c1-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-c1-cg-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-c1-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-cg-cg-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-ch-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-cg-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-c1-c2-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-c3-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-ca-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-cc-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-cd-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-ce-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-cf-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-cu-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-cv-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-cx-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-cy-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-n-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-n2-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-n3-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-n4-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-na-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-nb-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-nc-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-nd-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-ne-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-nf-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-nh-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-no-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-oh-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-os-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-p2-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-pb-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-pc-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-pd-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-pe-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-pf-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-p3-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-p4-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-px-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-p5-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-py-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-s2-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-sh-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-ss-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-s4-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-sx-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-s6-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-sy-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c2-c2-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c2-ce-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c2-cf-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-ce-cf-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-ce-ce-X fourier 1 1.0 2 180.0 # c2-c2 single bond, parm99 + dihedral_coeff @dihedral:X-cf-cf-X fourier 1 1.0 2 180.0 # c2-c2 single bond, parm99 + dihedral_coeff @dihedral:X-cc-cd-X fourier 1 4.0 2 180.0 # statistic value of parm94 + dihedral_coeff @dihedral:X-cc-cc-X fourier 1 4.0 2 180.0 # statistic value of parm94 + dihedral_coeff @dihedral:X-cd-cd-X fourier 1 4.0 2 180.0 # statistic value of parm94 + dihedral_coeff @dihedral:X-c2-c3-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c2-ca-X fourier 1 0.7 2 180.0 # optimized by Junmei Wang, March 2013 + dihedral_coeff @dihedral:X-c2-n-X fourier 1 0.65 2 180.0 # + dihedral_coeff @dihedral:X-c2-n2-X fourier 1 4.15 2 180.0 # double bond, parm99 + dihedral_coeff @dihedral:X-c2-ne-X fourier 1 4.15 2 180.0 # double bond, parm99 + dihedral_coeff @dihedral:X-c2-nf-X fourier 1 4.15 2 180.0 # double bond, parm99 + dihedral_coeff @dihedral:X-ce-ne-X fourier 1 0.8 2 180.0 # single bond + dihedral_coeff @dihedral:X-cf-nf-X fourier 1 0.8 2 180.0 # single bond + dihedral_coeff @dihedral:X-c2-nc-X fourier 1 4.75 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-c2-nd-X fourier 1 4.75 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-cc-nd-X fourier 1 4.75 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-cd-nc-X fourier 1 4.75 2 180.0 # statistiv value from parm94 + dihedral_coeff @dihedral:X-cc-nc-X fourier 1 4.75 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-cd-nd-X fourier 1 4.75 2 180.0 # statistiv value from parm94 + dihedral_coeff @dihedral:X-c2-n3-X fourier 1 0.3 2 180.0 # intrpol. + dihedral_coeff @dihedral:X-c2-n4-X fourier 1 0.0 3 180.0 # intrpol. + dihedral_coeff @dihedral:X-c2-na-X fourier 1 0.625 2 180.0 # + dihedral_coeff @dihedral:X-cc-na-X fourier 1 1.7 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-cd-na-X fourier 1 1.7 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-c2-nh-X fourier 1 0.675 2 180.0 # + dihedral_coeff @dihedral:X-c2-no-X fourier 1 0.75 2 180.0 # + dihedral_coeff @dihedral:X-c2-oh-X fourier 1 1.05 2 180.0 # parm99 + dihedral_coeff @dihedral:X-c2-os-X fourier 1 1.05 2 180.0 # parm99 + dihedral_coeff @dihedral:X-c2-p2-X fourier 1 6.65 2 180.0 # double bond + dihedral_coeff @dihedral:X-c2-pe-X fourier 1 6.65 2 180.0 # double bond + dihedral_coeff @dihedral:X-c2-pf-X fourier 1 6.65 2 180.0 # double bond + dihedral_coeff @dihedral:X-ce-pf-X fourier 1 6.65 2 180.0 # double bond + dihedral_coeff @dihedral:X-ce-pe-X fourier 1 0.95 2 180.0 # single bond + dihedral_coeff @dihedral:X-cf-pf-X fourier 1 0.95 2 180.0 # single bond + dihedral_coeff @dihedral:X-c2-pc-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-c2-pd-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-cc-pc-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-cc-pd-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-cd-pc-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-cd-pd-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-c2-p3-X fourier 1 0.45 2 180.0 # + dihedral_coeff @dihedral:X-c2-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!! + dihedral_coeff @dihedral:X-ce-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!! + dihedral_coeff @dihedral:X-cf-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!! + dihedral_coeff @dihedral:X-c2-px-X fourier 1 0.325 2 0.0 # + dihedral_coeff @dihedral:X-ce-px-X fourier 1 0.325 2 0.0 # + dihedral_coeff @dihedral:X-cf-px-X fourier 1 0.325 2 0.0 # + dihedral_coeff @dihedral:X-c2-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!! + dihedral_coeff @dihedral:X-ce-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!! + dihedral_coeff @dihedral:X-cf-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!! + dihedral_coeff @dihedral:X-c2-py-X fourier 1 1.43333333333 2 180.0 # + dihedral_coeff @dihedral:X-ce-py-X fourier 1 1.43333333333 2 180.0 # + dihedral_coeff @dihedral:X-cf-py-X fourier 1 1.43333333333 2 180.0 # + dihedral_coeff @dihedral:X-c2-sh-X fourier 1 0.5 2 180.0 # + dihedral_coeff @dihedral:X-c2-ss-X fourier 1 1.1 2 180.0 # + dihedral_coeff @dihedral:X-c2-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!! + dihedral_coeff @dihedral:X-ce-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!! + dihedral_coeff @dihedral:X-cf-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!! + dihedral_coeff @dihedral:X-c2-sx-X fourier 1 0.6 2 0.0 # + dihedral_coeff @dihedral:X-ce-sx-X fourier 1 0.6 2 0.0 # + dihedral_coeff @dihedral:X-cf-sx-X fourier 1 0.6 2 0.0 # + dihedral_coeff @dihedral:X-c2-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!! + dihedral_coeff @dihedral:X-ce-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!! + dihedral_coeff @dihedral:X-cf-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!! + dihedral_coeff @dihedral:X-c2-sy-X fourier 1 1.26666666667 2 180.0 # + dihedral_coeff @dihedral:X-ce-sy-X fourier 1 1.26666666667 2 180.0 # + dihedral_coeff @dihedral:X-cf-sy-X fourier 1 1.26666666667 2 180.0 # + dihedral_coeff @dihedral:X-c3-c3-X fourier 1 0.155555555556 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-cx-cx-X fourier 1 0.155555555556 3 0.0 # same as X-c3-c3-X + dihedral_coeff @dihedral:X-cy-cy-X fourier 1 0.155555555556 3 0.0 # same as X-c3-c3-X + dihedral_coeff @dihedral:X-c3-ca-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-n-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-cx-n-X fourier 1 0.0 2 0.0 # same as X-c3-n-X + dihedral_coeff @dihedral:X-cy-n-X fourier 1 0.0 2 0.0 # same as X-c3-n-X + dihedral_coeff @dihedral:X-c3-n2-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-ne-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-nf-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-n3-X fourier 1 0.3 3 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:X-c3-n4-X fourier 1 0.155555555556 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-na-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-nh-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-no-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-oh-X fourier 1 0.166666666667 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-os-X fourier 1 0.383333333333 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-p2-X fourier 1 0.266666666667 2 180.0 # + dihedral_coeff @dihedral:X-c3-pe-X fourier 1 0.266666666667 2 180.0 # + dihedral_coeff @dihedral:X-c3-pf-X fourier 1 0.266666666667 2 180.0 # + dihedral_coeff @dihedral:X-c3-p3-X fourier 1 0.133333333333 3 0.0 # + dihedral_coeff @dihedral:X-c3-p4-X fourier 1 0.133333333333 3 0.0 # + dihedral_coeff @dihedral:X-c3-px-X fourier 1 0.133333333333 3 0.0 # + dihedral_coeff @dihedral:X-c3-p5-X fourier 1 0.0222222222222 3 0.0 # + dihedral_coeff @dihedral:X-c3-py-X fourier 1 0.0222222222222 3 0.0 # + dihedral_coeff @dihedral:X-c3-sh-X fourier 1 0.25 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-ss-X fourier 1 0.333333333333 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-s4-X fourier 1 0.2 3 0.0 # + dihedral_coeff @dihedral:X-c3-sx-X fourier 1 0.2 3 0.0 # + dihedral_coeff @dihedral:X-c3-s6-X fourier 1 0.144444444444 3 0.0 # + dihedral_coeff @dihedral:X-c3-sy-X fourier 1 0.144444444444 3 0.0 # + dihedral_coeff @dihedral:X-c3-cc-X fourier 1 0.0 3 0.0 # same as X-c3-ca-X + dihedral_coeff @dihedral:X-c3-cd-X fourier 1 0.0 3 0.0 # same as X-c3-ca-X + dihedral_coeff @dihedral:X-ca-ca-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-ca-cp-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-ca-cq-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-cp-cp-X fourier 1 1.0 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-cq-cq-X fourier 1 1.0 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-ca-n-X fourier 1 0.45 2 180.0 # + dihedral_coeff @dihedral:X-ca-n2-X fourier 1 0.0 3 180.0 # + dihedral_coeff @dihedral:X-ca-ne-X fourier 1 0.0 3 180.0 # + dihedral_coeff @dihedral:X-ca-nf-X fourier 1 0.0 3 180.0 # + dihedral_coeff @dihedral:X-ca-n4-X fourier 1 1.75 2 0.0 # + dihedral_coeff @dihedral:X-ca-na-X fourier 1 0.3 2 180.0 # + dihedral_coeff @dihedral:X-ca-nb-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X + dihedral_coeff @dihedral:X-ca-nc-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X + dihedral_coeff @dihedral:X-ca-nd-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X + dihedral_coeff @dihedral:X-ca-nh-X fourier 1 1.05 2 180.0 # + dihedral_coeff @dihedral:X-cc-nh-X fourier 1 1.05 2 180.0 # same as X-ca-nh-X + dihedral_coeff @dihedral:X-cd-nh-X fourier 1 1.05 2 180.0 # same as X-ca-nh-X + dihedral_coeff @dihedral:X-ca-no-X fourier 1 0.6 2 180.0 # + dihedral_coeff @dihedral:X-ca-oh-X fourier 1 0.9 2 180.0 # Junmei et al, 99 + dihedral_coeff @dihedral:X-ca-os-X fourier 1 0.9 2 180.0 # same as X-ca-oh-X + dihedral_coeff @dihedral:X-ca-p2-X fourier 1 0.6 2 180.0 # + dihedral_coeff @dihedral:X-ca-pe-X fourier 1 0.6 2 180.0 # same as X-ca-p2-X + dihedral_coeff @dihedral:X-ca-pf-X fourier 1 0.6 2 180.0 # same as X-ca-p2-X + dihedral_coeff @dihedral:X-ca-pc-X fourier 1 4.8 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-ca-pd-X fourier 1 4.8 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-ca-p3-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-ca-p4-X fourier 1 0.525 2 180.0 # + dihedral_coeff @dihedral:X-ca-px-X fourier 1 0.525 2 180.0 # estimated, same as X-ca-p4-X + dihedral_coeff @dihedral:X-ca-p5-X fourier 1 1.46666666667 2 180.0 # + dihedral_coeff @dihedral:X-ca-py-X fourier 1 1.46666666667 2 180.0 # estimated, same as X-ca-p5-X + dihedral_coeff @dihedral:X-ca-sh-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-ca-ss-X fourier 1 0.4 2 180.0 # + dihedral_coeff @dihedral:X-ca-s4-X fourier 1 0.3 2 0.0 # + dihedral_coeff @dihedral:X-ca-sx-X fourier 1 0.3 2 0.0 # estimated, same as X-ca-s4-X + dihedral_coeff @dihedral:X-ca-s6-X fourier 1 1.3 2 180.0 # + dihedral_coeff @dihedral:X-ca-sy-X fourier 1 1.3 2 180.0 # estimated, same as X-ca-s6-X + dihedral_coeff @dihedral:X-n-cc-X fourier 1 1.65 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-n-cd-X fourier 1 1.65 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-n-n-X fourier 1 1.15 2 0.0 # + dihedral_coeff @dihedral:X-n-n2-X fourier 1 0.4 2 0.0 # + dihedral_coeff @dihedral:X-n-ne-X fourier 1 0.4 2 0.0 # + dihedral_coeff @dihedral:X-n-nf-X fourier 1 0.4 2 0.0 # + dihedral_coeff @dihedral:X-n-n3-X fourier 1 1.075 2 0.0 # + dihedral_coeff @dihedral:X-n-n4-X fourier 1 0.95 2 0.0 # + dihedral_coeff @dihedral:X-n-na-X fourier 1 0.7 2 0.0 # + dihedral_coeff @dihedral:X-n-nc-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n-nd-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n-nh-X fourier 1 1.1 2 0.0 # + dihedral_coeff @dihedral:X-n-no-X fourier 1 1.375 2 180.0 # + dihedral_coeff @dihedral:X-n-oh-X fourier 1 1.5 2 0.0 # + dihedral_coeff @dihedral:X-n-os-X fourier 1 1.1 2 0.0 # + dihedral_coeff @dihedral:X-n-p2-X fourier 1 1.0 2 180.0 # + dihedral_coeff @dihedral:X-n-pe-X fourier 1 1.0 2 180.0 # + dihedral_coeff @dihedral:X-n-pf-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n-pc-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n-pd-X fourier 1 1.0 2 180.0 # + dihedral_coeff @dihedral:X-n-p3-X fourier 1 2.25 2 0.0 # + dihedral_coeff @dihedral:X-n-p4-X fourier 1 0.325 2 0.0 # + dihedral_coeff @dihedral:X-n-px-X fourier 1 0.325 2 0.0 # + dihedral_coeff @dihedral:X-n-p5-X fourier 1 2.2 2 180.0 # + dihedral_coeff @dihedral:X-n-py-X fourier 1 2.2 2 180.0 # + dihedral_coeff @dihedral:X-n-sh-X fourier 1 1.1 2 0.0 # + dihedral_coeff @dihedral:X-n-ss-X fourier 1 1.5 2 0.0 # + dihedral_coeff @dihedral:X-n-s4-X fourier 1 1.5 3 0.0 # + dihedral_coeff @dihedral:X-n-sx-X fourier 1 1.5 3 0.0 # + dihedral_coeff @dihedral:X-n-s6-X fourier 1 1.1 2 180.0 # + dihedral_coeff @dihedral:X-n-sy-X fourier 1 1.1 2 180.0 # + dihedral_coeff @dihedral:X-n1-c2-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-c3-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-ca-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-cc-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-cd-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-ce-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-cf-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-cu-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-cv-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-cx-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-cy-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-n-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-n1-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-n2-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-n3-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-n4-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-na-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-nb-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-nc-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-nd-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-ne-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-nf-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-nh-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-no-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-oh-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-os-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-p2-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-pb-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-pc-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-pd-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-pe-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-pf-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-p3-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-p4-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-px-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-p5-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-py-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-s2-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-sh-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-ss-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-s4-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-sx-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-s6-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-sy-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n2-n2-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond + dihedral_coeff @dihedral:X-n2-ne-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond + dihedral_coeff @dihedral:X-n2-nf-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond + dihedral_coeff @dihedral:X-ne-nf-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond + dihedral_coeff @dihedral:X-ne-ne-X fourier 1 1.2 2 180.0 # single bond, intrpol + dihedral_coeff @dihedral:X-nf-nf-X fourier 1 1.2 2 180.0 # single bond, intrpol + dihedral_coeff @dihedral:X-nc-nc-X fourier 1 4.0 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-nd-nd-X fourier 1 4.0 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-nc-nd-X fourier 1 4.0 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-n2-nc-X fourier 2 3.0 2 180.0 2.8 1 0.0 # same as X-n2-n2-X + dihedral_coeff @dihedral:X-n2-nd-X fourier 2 3.0 2 180.0 2.8 1 0.0 # same as X-n2-n2-X + dihedral_coeff @dihedral:X-n2-n3-X fourier 1 6.1 2 180.0 # + dihedral_coeff @dihedral:X-ne-n3-X fourier 1 6.1 2 180.0 # + dihedral_coeff @dihedral:X-nf-n3-X fourier 1 6.1 2 180.0 # + dihedral_coeff @dihedral:X-n2-n4-X fourier 1 8.0 2 180.0 # + dihedral_coeff @dihedral:X-ne-n4-X fourier 1 8.0 2 180.0 # + dihedral_coeff @dihedral:X-nf-n4-X fourier 1 8.0 2 180.0 # + dihedral_coeff @dihedral:X-n2-na-X fourier 1 1.7 2 180.0 # + dihedral_coeff @dihedral:X-ne-na-X fourier 1 1.7 2 180.0 # + dihedral_coeff @dihedral:X-nf-na-X fourier 1 1.7 2 180.0 # + dihedral_coeff @dihedral:X-na-nc-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-na-nd-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-nh-X fourier 1 2.8 2 180.0 # + dihedral_coeff @dihedral:X-ne-nh-X fourier 1 2.8 2 180.0 # + dihedral_coeff @dihedral:X-nf-nh-X fourier 1 2.8 2 180.0 # + dihedral_coeff @dihedral:X-n2-no-X fourier 1 0.75 2 180.0 # + dihedral_coeff @dihedral:X-ne-no-X fourier 1 0.75 2 180.0 # + dihedral_coeff @dihedral:X-nf-no-X fourier 1 0.75 2 180.0 # + dihedral_coeff @dihedral:X-n2-oh-X fourier 1 3.2 2 180.0 # + dihedral_coeff @dihedral:X-ne-oh-X fourier 1 3.2 2 180.0 # + dihedral_coeff @dihedral:X-nf-oh-X fourier 1 3.2 2 180.0 # + dihedral_coeff @dihedral:X-n2-os-X fourier 1 3.0 2 180.0 # + dihedral_coeff @dihedral:X-ne-os-X fourier 1 3.0 2 180.0 # + dihedral_coeff @dihedral:X-nf-os-X fourier 1 3.0 2 180.0 # + dihedral_coeff @dihedral:X-nc-os-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nc-ss-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-pe-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-pf-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-ne-pf-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-pc-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-pd-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nc-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nd-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nc-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nd-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nd-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nc-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-ne-pe-X fourier 1 0.6 1 0.0 # single bond + dihedral_coeff @dihedral:X-nf-pf-X fourier 1 0.6 1 0.0 # single bond + dihedral_coeff @dihedral:X-n2-p3-X fourier 1 2.1 2 180.0 # + dihedral_coeff @dihedral:X-n2-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-ne-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-nf-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-n2-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-ne-p5-X fourier 1 1.0 3 180.0 # + dihedral_coeff @dihedral:X-nf-p5-X fourier 1 1.0 3 180.0 # + dihedral_coeff @dihedral:X-ne-px-X fourier 1 1.0 3 180.0 # + dihedral_coeff @dihedral:X-nf-px-X fourier 1 1.0 3 180.0 # + dihedral_coeff @dihedral:X-n2-sh-X fourier 1 2.1 2 180.0 # + dihedral_coeff @dihedral:X-ne-sh-X fourier 1 2.1 2 180.0 # + dihedral_coeff @dihedral:X-nf-sh-X fourier 1 2.1 2 180.0 # + dihedral_coeff @dihedral:X-n2-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 # + dihedral_coeff @dihedral:X-ne-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 # + dihedral_coeff @dihedral:X-nf-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 # + dihedral_coeff @dihedral:X-n2-s4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-ne-sx-X fourier 1 1.5 3 180.0 # + dihedral_coeff @dihedral:X-nf-sx-X fourier 1 1.5 3 180.0 # + dihedral_coeff @dihedral:X-n2-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-ne-sy-X fourier 2 0.5 3 180.0 6.8 1 180.0 # + dihedral_coeff @dihedral:X-nf-sy-X fourier 2 0.5 3 180.0 6.8 1 180.0 # + dihedral_coeff @dihedral:X-n3-n3-X fourier 1 2.25 2 0.0 # + dihedral_coeff @dihedral:X-n3-n4-X fourier 1 0.25 3 0.0 # + dihedral_coeff @dihedral:X-n3-na-X fourier 1 1.6 2 0.0 # + dihedral_coeff @dihedral:X-n3-nh-X fourier 1 1.9 2 0.0 # + dihedral_coeff @dihedral:X-n3-no-X fourier 1 4.0 2 180.0 # + dihedral_coeff @dihedral:X-n3-oh-X fourier 1 2.2 2 0.0 # + dihedral_coeff @dihedral:X-n3-os-X fourier 1 1.8 2 0.0 # + dihedral_coeff @dihedral:X-n3-p2-X fourier 1 3.2 2 180.0 # + dihedral_coeff @dihedral:X-n3-pe-X fourier 1 3.2 2 180.0 # + dihedral_coeff @dihedral:X-n3-pf-X fourier 1 3.2 2 180.0 # + dihedral_coeff @dihedral:X-n3-p3-X fourier 1 2.35 2 0.0 # + dihedral_coeff @dihedral:X-n3-p4-X fourier 1 2.1 2 180.0 # + dihedral_coeff @dihedral:X-n3-px-X fourier 1 2.1 2 180.0 # + dihedral_coeff @dihedral:X-n3-p5-X fourier 1 3.0 2 180.0 # + dihedral_coeff @dihedral:X-n3-py-X fourier 1 3.0 2 180.0 # + dihedral_coeff @dihedral:X-n3-sh-X fourier 1 3.1 2 0.0 # + dihedral_coeff @dihedral:X-n3-ss-X fourier 1 2.6 2 0.0 # + dihedral_coeff @dihedral:X-n3-s4-X fourier 1 3.75 2 0.0 # + dihedral_coeff @dihedral:X-n3-sx-X fourier 1 3.75 2 0.0 # + dihedral_coeff @dihedral:X-n3-s6-X fourier 1 3.13333333333 2 0.0 # + dihedral_coeff @dihedral:X-n3-sy-X fourier 1 3.13333333333 2 0.0 # + dihedral_coeff @dihedral:X-n4-n4-X fourier 1 0.188888888889 3 0.0 # + dihedral_coeff @dihedral:X-n4-na-X fourier 1 0.233333333333 3 0.0 # + dihedral_coeff @dihedral:X-n4-nh-X fourier 1 0.183333333333 3 0.0 # + dihedral_coeff @dihedral:X-n4-no-X fourier 1 0.0833333333333 3 180.0 # + dihedral_coeff @dihedral:X-n4-oh-X fourier 1 0.333333333333 3 0.0 # + dihedral_coeff @dihedral:X-n4-os-X fourier 1 0.566666666667 3 0.0 # + dihedral_coeff @dihedral:X-n4-p2-X fourier 1 0.166666666667 3 180.0 # + dihedral_coeff @dihedral:X-n4-pe-X fourier 1 0.166666666667 3 180.0 # + dihedral_coeff @dihedral:X-n4-pf-X fourier 1 0.166666666667 3 180.0 # + dihedral_coeff @dihedral:X-n4-p3-X fourier 1 0.15 3 0.0 # + dihedral_coeff @dihedral:X-n4-p4-X fourier 1 0.05 3 0.0 # + dihedral_coeff @dihedral:X-n4-px-X fourier 1 0.05 3 0.0 # + dihedral_coeff @dihedral:X-n4-p5-X fourier 1 0.0888888888889 3 0.0 # + dihedral_coeff @dihedral:X-n4-py-X fourier 1 0.0888888888889 3 0.0 # + dihedral_coeff @dihedral:X-n4-sh-X fourier 1 0.666666666667 3 0.0 # + dihedral_coeff @dihedral:X-n4-ss-X fourier 1 0.333333333333 3 0.0 # + dihedral_coeff @dihedral:X-n4-s4-X fourier 1 0.283333333333 3 0.0 # + dihedral_coeff @dihedral:X-n4-sx-X fourier 1 0.283333333333 3 0.0 # + dihedral_coeff @dihedral:X-n4-s6-X fourier 1 0.133333333333 3 0.0 # + dihedral_coeff @dihedral:X-n4-sy-X fourier 1 0.133333333333 3 0.0 # + dihedral_coeff @dihedral:X-na-na-X fourier 1 0.9 2 0.0 # + dihedral_coeff @dihedral:X-na-nh-X fourier 1 1.2 2 0.0 # + dihedral_coeff @dihedral:X-na-no-X fourier 1 6.0 2 180.0 # + dihedral_coeff @dihedral:X-na-oh-X fourier 1 1.0 2 0.0 # + dihedral_coeff @dihedral:X-na-os-X fourier 1 0.65 2 0.0 # + dihedral_coeff @dihedral:X-na-p2-X fourier 1 1.0 2 180.0 # + dihedral_coeff @dihedral:X-na-pe-X fourier 1 1.0 2 180.0 # + dihedral_coeff @dihedral:X-na-pf-X fourier 1 1.0 2 180.0 # + dihedral_coeff @dihedral:X-na-p3-X fourier 1 1.45 2 0.0 # + dihedral_coeff @dihedral:X-na-p4-X fourier 1 1.1 3 0.0 # + dihedral_coeff @dihedral:X-na-px-X fourier 1 1.1 3 0.0 # + dihedral_coeff @dihedral:X-na-p5-X fourier 1 0.833333333333 2 180.0 # + dihedral_coeff @dihedral:X-na-py-X fourier 1 0.833333333333 2 180.0 # + dihedral_coeff @dihedral:X-na-sh-X fourier 1 1.8 2 0.0 # + dihedral_coeff @dihedral:X-na-ss-X fourier 1 7.8 2 0.0 # + dihedral_coeff @dihedral:X-na-s4-X fourier 1 1.05 2 0.0 # + dihedral_coeff @dihedral:X-na-sx-X fourier 1 1.05 2 0.0 # + dihedral_coeff @dihedral:X-na-s6-X fourier 1 3.66666666667 2 180.0 # + dihedral_coeff @dihedral:X-na-sy-X fourier 1 3.66666666667 2 180.0 # + dihedral_coeff @dihedral:X-nh-nh-X fourier 1 1.8 3 180.0 # + dihedral_coeff @dihedral:X-nh-no-X fourier 1 2.55 2 180.0 # + dihedral_coeff @dihedral:X-nh-oh-X fourier 1 1.5 2 0.0 # + dihedral_coeff @dihedral:X-nh-os-X fourier 1 1.5 1 0.0 # + dihedral_coeff @dihedral:X-nh-p2-X fourier 1 1.4 2 180.0 # + dihedral_coeff @dihedral:X-nh-pe-X fourier 1 1.4 2 180.0 # + dihedral_coeff @dihedral:X-nh-pf-X fourier 1 1.4 2 180.0 # + dihedral_coeff @dihedral:X-nh-p3-X fourier 1 2.35 2 0.0 # + dihedral_coeff @dihedral:X-nh-p4-X fourier 1 1.175 3 0.0 # + dihedral_coeff @dihedral:X-nh-px-X fourier 1 1.175 3 0.0 # + dihedral_coeff @dihedral:X-nh-p5-X fourier 1 0.8 2 0.0 # + dihedral_coeff @dihedral:X-nh-py-X fourier 1 0.8 2 0.0 # + dihedral_coeff @dihedral:X-nh-sh-X fourier 1 1.6 2 0.0 # + dihedral_coeff @dihedral:X-nh-ss-X fourier 1 2.1 2 0.0 # + dihedral_coeff @dihedral:X-nh-s4-X fourier 2 0.75 2 0.0 0.1 3 180.0 # + dihedral_coeff @dihedral:X-nh-sx-X fourier 2 0.75 2 0.0 0.1 3 180.0 # + dihedral_coeff @dihedral:X-nh-s6-X fourier 1 0.1 2 180.0 # + dihedral_coeff @dihedral:X-nh-sy-X fourier 1 0.1 2 180.0 # + dihedral_coeff @dihedral:X-no-no-X fourier 2 0.4 4 180.0 1.8 2 180.0 # + dihedral_coeff @dihedral:X-no-oh-X fourier 1 3.9 2 180.0 # + dihedral_coeff @dihedral:X-no-os-X fourier 1 3.0 2 180.0 # + dihedral_coeff @dihedral:X-no-p2-X fourier 1 0.3 2 180.0 # + dihedral_coeff @dihedral:X-no-pe-X fourier 1 0.3 2 180.0 # + dihedral_coeff @dihedral:X-no-pf-X fourier 1 0.3 2 180.0 # + dihedral_coeff @dihedral:X-no-p3-X fourier 1 1.9 2 180.0 # + dihedral_coeff @dihedral:X-no-p4-X fourier 1 0.575 2 180.0 # + dihedral_coeff @dihedral:X-no-px-X fourier 1 0.575 2 180.0 # + dihedral_coeff @dihedral:X-no-p5-X fourier 2 2.4 2 0.0 0.4 3 0.0 # + dihedral_coeff @dihedral:X-no-py-X fourier 2 2.4 2 0.0 0.4 3 0.0 # + dihedral_coeff @dihedral:X-no-sh-X fourier 1 2.3 2 180.0 # + dihedral_coeff @dihedral:X-no-ss-X fourier 1 2.7 2 180.0 # + dihedral_coeff @dihedral:X-no-s4-X fourier 1 2.6 2 180.0 # + dihedral_coeff @dihedral:X-no-sx-X fourier 1 2.6 2 180.0 # + dihedral_coeff @dihedral:X-no-s6-X fourier 1 0.333333333333 2 0.0 # + dihedral_coeff @dihedral:X-no-sy-X fourier 1 0.333333333333 2 0.0 # + dihedral_coeff @dihedral:X-oh-oh-X fourier 1 1.6 2 0.0 # + dihedral_coeff @dihedral:X-oh-os-X fourier 1 1.6 2 0.0 # + dihedral_coeff @dihedral:X-oh-p2-X fourier 1 1.5 2 180.0 # + dihedral_coeff @dihedral:X-oh-pe-X fourier 1 1.5 2 180.0 # + dihedral_coeff @dihedral:X-oh-pf-X fourier 1 1.5 2 180.0 # + dihedral_coeff @dihedral:X-oh-p3-X fourier 1 0.4 3 180.0 # + dihedral_coeff @dihedral:X-oh-p4-X fourier 1 0.7 1 0.0 # + dihedral_coeff @dihedral:X-oh-px-X fourier 1 0.7 1 0.0 # + dihedral_coeff @dihedral:X-oh-p5-X fourier 1 0.533333333333 3 0.0 # + dihedral_coeff @dihedral:X-oh-py-X fourier 1 0.533333333333 3 0.0 # + dihedral_coeff @dihedral:X-oh-sh-X fourier 1 2.4 2 0.0 # + dihedral_coeff @dihedral:X-oh-ss-X fourier 1 2.4 2 0.0 # + dihedral_coeff @dihedral:X-oh-s4-X fourier 1 5.0 1 0.0 # + dihedral_coeff @dihedral:X-oh-sx-X fourier 1 5.0 1 0.0 # + dihedral_coeff @dihedral:X-oh-s6-X fourier 1 9.5 1 180.0 # + dihedral_coeff @dihedral:X-oh-sy-X fourier 1 9.5 1 180.0 # + dihedral_coeff @dihedral:X-os-os-X fourier 1 1.0 1 0.0 # + dihedral_coeff @dihedral:X-os-ss-X fourier 1 2.2 2 0.0 # + dihedral_coeff @dihedral:X-os-sh-X fourier 1 1.8 2 0.0 # + dihedral_coeff @dihedral:X-os-s4-X fourier 1 1.65 3 0.0 # + dihedral_coeff @dihedral:X-os-sx-X fourier 1 1.65 3 0.0 # + dihedral_coeff @dihedral:X-os-s6-X fourier 1 1.2 2 180.0 # + dihedral_coeff @dihedral:X-os-sy-X fourier 1 1.2 2 180.0 # + dihedral_coeff @dihedral:X-os-p2-X fourier 2 3.0 2 180.0 2.0 1 180.0 # + dihedral_coeff @dihedral:X-os-pe-X fourier 2 3.0 2 180.0 2.0 1 180.0 # + dihedral_coeff @dihedral:X-os-pf-X fourier 2 3.0 2 180.0 2.0 1 180.0 # + dihedral_coeff @dihedral:X-os-p3-X fourier 1 2.2 2 0.0 # + dihedral_coeff @dihedral:X-os-p4-X fourier 1 1.05 2 180.0 # + dihedral_coeff @dihedral:X-os-px-X fourier 1 1.05 2 180.0 # + dihedral_coeff @dihedral:X-os-p5-X fourier 1 0.8 2 0.0 # + dihedral_coeff @dihedral:X-os-py-X fourier 1 0.8 2 0.0 # + dihedral_coeff @dihedral:X-p2-p2-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-pe-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-pf-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-pe-pe-X fourier 1 1.2 2 180.0 # single bond + dihedral_coeff @dihedral:X-pf-pf-X fourier 1 1.2 2 180.0 # single bond + dihedral_coeff @dihedral:X-pc-pc-X fourier 1 7.2 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-pd-pd-X fourier 1 7.2 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-pc-pd-X fourier 1 7.2 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-p3-X fourier 1 1.2 1 0.0 # + dihedral_coeff @dihedral:X-pe-p3-X fourier 1 1.2 1 0.0 # + dihedral_coeff @dihedral:X-pf-p3-X fourier 1 1.2 1 0.0 # + dihedral_coeff @dihedral:X-p2-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-pe-px-X fourier 1 2.45 2 0.0 # + dihedral_coeff @dihedral:X-pf-px-X fourier 1 2.45 2 0.0 # + dihedral_coeff @dihedral:X-p2-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-pe-py-X fourier 1 1.9 1 0.0 # + dihedral_coeff @dihedral:X-pf-py-X fourier 1 1.9 1 0.0 # + dihedral_coeff @dihedral:X-p2-sh-X fourier 1 1.4 2 180.0 # + dihedral_coeff @dihedral:X-pe-sh-X fourier 1 1.4 2 180.0 # + dihedral_coeff @dihedral:X-pf-sh-X fourier 1 1.4 2 180.0 # + dihedral_coeff @dihedral:X-p2-ss-X fourier 1 1.4 2 180.0 # + dihedral_coeff @dihedral:X-pe-ss-X fourier 1 1.4 2 180.0 # + dihedral_coeff @dihedral:X-pf-ss-X fourier 1 1.4 2 180.0 # + dihedral_coeff @dihedral:X-p2-s4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-pe-sx-X fourier 1 1.5 2 0.0 # + dihedral_coeff @dihedral:X-pf-sx-X fourier 1 1.5 2 0.0 # + dihedral_coeff @dihedral:X-p2-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-pe-sy-X fourier 1 0.4 3 180.0 # + dihedral_coeff @dihedral:X-pf-sy-X fourier 1 0.4 3 180.0 # + dihedral_coeff @dihedral:X-p3-p3-X fourier 1 0.5 3 0.0 # + dihedral_coeff @dihedral:X-p3-p4-X fourier 1 0.9 1 0.0 # + dihedral_coeff @dihedral:X-p3-px-X fourier 1 0.9 1 0.0 # + dihedral_coeff @dihedral:X-p3-p5-X fourier 1 1.83333333333 2 180.0 # + dihedral_coeff @dihedral:X-p3-py-X fourier 1 1.83333333333 2 180.0 # + dihedral_coeff @dihedral:X-p3-sh-X fourier 1 4.6 2 0.0 # + dihedral_coeff @dihedral:X-p3-ss-X fourier 1 1.15 3 0.0 # + dihedral_coeff @dihedral:X-p3-s4-X fourier 1 3.85 2 0.0 # + dihedral_coeff @dihedral:X-p3-sx-X fourier 1 3.85 2 0.0 # + dihedral_coeff @dihedral:X-p3-s6-X fourier 1 0.266666666667 3 0.0 # + dihedral_coeff @dihedral:X-p3-sy-X fourier 1 0.266666666667 3 0.0 # + dihedral_coeff @dihedral:X-p4-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-px-px-X fourier 1 1.45 2 180.0 # + dihedral_coeff @dihedral:X-p4-p5-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-px-py-X fourier 1 0.316666666667 2 180.0 # + dihedral_coeff @dihedral:X-p4-s4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-px-sx-X fourier 1 0.85 1 0.0 # + dihedral_coeff @dihedral:X-p4-s6-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-px-sy-X fourier 1 0.116666666667 3 0.0 # + dihedral_coeff @dihedral:X-p4-sh-X fourier 1 0.25 1 180.0 # + dihedral_coeff @dihedral:X-px-sh-X fourier 1 0.25 1 180.0 # + dihedral_coeff @dihedral:X-p4-ss-X fourier 1 0.6 2 180.0 # + dihedral_coeff @dihedral:X-px-ss-X fourier 1 0.6 2 180.0 # + dihedral_coeff @dihedral:X-p5-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-py-py-X fourier 1 0.6 2 0.0 # + dihedral_coeff @dihedral:X-p5-sh-X fourier 1 0.3 3 0.0 # + dihedral_coeff @dihedral:X-py-sh-X fourier 1 0.3 3 0.0 # + dihedral_coeff @dihedral:X-p5-ss-X fourier 1 3.8 2 180.0 # + dihedral_coeff @dihedral:X-py-ss-X fourier 1 3.8 2 180.0 # + dihedral_coeff @dihedral:X-p5-s4-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-py-sx-X fourier 1 0.266666666667 3 0.0 # + dihedral_coeff @dihedral:X-p5-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-py-sy-X fourier 1 0.277777777778 3 0.0 # + dihedral_coeff @dihedral:X-sh-sh-X fourier 1 5.6 3 0.0 # + dihedral_coeff @dihedral:X-sh-ss-X fourier 1 5.3 3 0.0 # + dihedral_coeff @dihedral:X-sh-s4-X fourier 1 0.7 3 0.0 # + dihedral_coeff @dihedral:X-sh-sx-X fourier 1 0.7 3 0.0 # + dihedral_coeff @dihedral:X-sh-s6-X fourier 1 4.66666666667 2 180.0 # + dihedral_coeff @dihedral:X-sh-sy-X fourier 1 4.66666666667 2 180.0 # + dihedral_coeff @dihedral:X-ss-ss-X fourier 1 0.0 3 0.0 # + dihedral_coeff @dihedral:X-ss-s4-X fourier 1 0.3 3 0.0 # + dihedral_coeff @dihedral:X-ss-sx-X fourier 1 0.3 3 0.0 # + dihedral_coeff @dihedral:X-ss-s6-X fourier 1 3.06666666667 2 180.0 # + dihedral_coeff @dihedral:X-ss-sy-X fourier 1 3.06666666667 2 180.0 # + dihedral_coeff @dihedral:X-s4-s4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-sx-sx-X fourier 1 0.625 3 0.0 # + dihedral_coeff @dihedral:X-s4-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-sx-sy-X fourier 1 4.33333333333 2 180.0 # + dihedral_coeff @dihedral:X-s6-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-sy-sy-X fourier 1 0.155555555556 2 180.0 # + dihedral_coeff @dihedral:c3-c-sh-hs fourier 2 2.25 2 180.0 1.3 1 180.0 # + dihedral_coeff @dihedral:c2-c2-ss-c3 fourier 2 1.1 2 180.0 0.7 3 180.0 # + dihedral_coeff @dihedral:c2-c2-n-c fourier 2 0.65 2 180.0 1.2 1 180.0 # + dihedral_coeff @dihedral:c-n-p2-c2 fourier 2 1.0 2 180.0 1.9 1 180.0 # + dihedral_coeff @dihedral:n-c3-c-n fourier 2 1.7 1 180.0 2.0 2 180.0 # + dihedral_coeff @dihedral:c-n-c3-c fourier 2 0.85 2 180.0 0.8 1 0.0 # + dihedral_coeff @dihedral:c3-c3-n-c fourier 3 0.5 4 180.0 0.15 3 180.0 0.53 1 0.0 # phi,psi,parm94 + dihedral_coeff @dihedral:c3-c3-c-n fourier 2 0.1 4 0.0 0.07 2 0.0 # phi,psi,parm94 + dihedral_coeff @dihedral:c2-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # + dihedral_coeff @dihedral:c2-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # + dihedral_coeff @dihedral:ce-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # + dihedral_coeff @dihedral:ce-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # + dihedral_coeff @dihedral:cf-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # + dihedral_coeff @dihedral:cf-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # + dihedral_coeff @dihedral:hn-n-c-o fourier 2 2.5 2 180.0 2.0 1 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:c3-ss-ss-c3 fourier 2 3.5 2 0.0 0.6 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:c3-n3-nh-ca fourier 2 1.9 2 0.0 1.9 3 0.0 # + dihedral_coeff @dihedral:c3-n3-p5-o fourier 2 3.0 2 180.0 2.3 3 0.0 # + dihedral_coeff @dihedral:ca-nh-oh-ho fourier 2 1.2 1 0.0 1.5 2 0.0 # + dihedral_coeff @dihedral:oh-p5-os-c3 fourier 2 0.25 3 0.0 1.2 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:os-p5-os-c3 fourier 2 0.25 3 0.0 1.2 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:h1-c3-c-o fourier 2 0.8 1 0.0 0.08 3 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:hc-c3-c-o fourier 2 0.8 1 0.0 0.08 3 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:hc-c3-c3-hc fourier 1 0.15 3 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:hc-c3-c3-c3 fourier 1 0.16 3 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:hc-c3-c2-c2 fourier 2 0.38 3 180.0 1.15 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:ho-oh-c3-c3 fourier 2 0.16 3 0.0 0.25 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:ho-oh-c-o fourier 2 2.3 2 180.0 1.9 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:c2-c2-c-o fourier 2 2.175 2 180.0 0.3 3 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:c3-c2-c2-c3 fourier 2 6.65 2 180.0 1.9 1 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:c3-c3-c3-c3 fourier 3 0.18 3 0.0 0.25 2 180.0 0.2 1 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:c3-c3-n3-c3 fourier 2 0.3 3 0.0 0.48 2 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:c3-c3-os-c3 fourier 2 0.383 3 0.0 0.1 2 180.0 # + dihedral_coeff @dihedral:c3-c3-os-c fourier 2 0.383 3 0.0 0.8 1 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:c3-os-c3-os fourier 3 0.1 3 0.0 0.85 2 180.0 1.35 1 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:c3-os-c3-na fourier 2 0.383 3 0.0 0.65 2 0.0 # parm98.dat, TC,PC,PAK + dihedral_coeff @dihedral:o-c-os-c3 fourier 2 2.7 2 180.0 1.4 1 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:os-c3-na-c2 fourier 2 0.0 2 0.0 2.5 1 0.0 # parm98, TC,PC,PAK + dihedral_coeff @dihedral:os-c3-c3-os fourier 2 0.144 3 0.0 1.175 2 0.0 # parm98, TC,PC,PAK + dihedral_coeff @dihedral:os-c3-c3-oh fourier 2 0.144 3 0.0 1.175 2 0.0 # parm98, TC,PC,PAK + dihedral_coeff @dihedral:oh-c3-c3-oh fourier 2 0.144 3 0.0 1.175 2 0.0 # parm98, TC,PC,PAK + dihedral_coeff @dihedral:f-c3-c3-f fourier 2 0.0 3 0.0 1.2 1 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:cl-c3-c3-cl fourier 2 0.0 3 0.0 0.45 1 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:br-c3-c3-br fourier 2 0.0 3 0.0 0.0 1 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:h1-c3-c3-os fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:h1-c3-c3-oh fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:h1-c3-c3-f fourier 2 0.0 3 0.0 0.19 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:h1-c3-c3-cl fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:h1-c3-c3-br fourier 2 0.0 3 0.0 0.55 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:hc-c3-c3-os fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:hc-c3-c3-oh fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:hc-c3-c3-f fourier 2 0.0 3 0.0 0.19 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:hc-c3-c3-cl fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:hc-c3-c3-br fourier 2 0.0 3 0.0 0.55 1 0.0 # Junmei et al, 1999 + } # (end of dihedral_coeffs) + + write_once("Data Dihedrals By Type") { + @dihedral:X-c-c-X @atom:* @atom:c @atom:c @atom:* + @dihedral:X-c-c1-X @atom:* @atom:c @atom:c1 @atom:* + @dihedral:X-c-cg-X @atom:* @atom:c @atom:cg @atom:* + @dihedral:X-c-ch-X @atom:* @atom:c @atom:ch @atom:* + @dihedral:X-c-c2-X @atom:* @atom:c @atom:c2 @atom:* + @dihedral:X-c-cu-X @atom:* @atom:c @atom:cu @atom:* + @dihedral:X-c-cv-X @atom:* @atom:c @atom:cv @atom:* + @dihedral:X-c-ce-X @atom:* @atom:c @atom:ce @atom:* + @dihedral:X-c-cf-X @atom:* @atom:c @atom:cf @atom:* + @dihedral:X-c-c3-X @atom:* @atom:c @atom:c3 @atom:* + @dihedral:X-c-cx-X @atom:* @atom:c @atom:cx @atom:* + @dihedral:X-c-cy-X @atom:* @atom:c @atom:cy @atom:* + @dihedral:X-c-ca-X @atom:* @atom:c @atom:ca @atom:* + @dihedral:X-c-cc-X @atom:* @atom:c @atom:cc @atom:* + @dihedral:X-c-cd-X @atom:* @atom:c @atom:cd @atom:* + @dihedral:X-c-n-X @atom:* @atom:c @atom:n @atom:* + @dihedral:X-c-n2-X @atom:* @atom:c @atom:n2 @atom:* + @dihedral:X-c-nc-X @atom:* @atom:c @atom:nc @atom:* + @dihedral:X-c-nd-X @atom:* @atom:c @atom:nd @atom:* + @dihedral:X-c-ne-X @atom:* @atom:c @atom:ne @atom:* + @dihedral:X-c-nf-X @atom:* @atom:c @atom:nf @atom:* + @dihedral:X-c-na-X @atom:* @atom:c @atom:na @atom:* + @dihedral:X-c-na-X @atom:* @atom:c @atom:na @atom:* + @dihedral:X-c-no-X @atom:* @atom:c @atom:no @atom:* + @dihedral:X-c-oh-X @atom:* @atom:c @atom:oh @atom:* + @dihedral:X-c-os-X @atom:* @atom:c @atom:os @atom:* + @dihedral:X-c-p2-X @atom:* @atom:c @atom:p2 @atom:* + @dihedral:X-c-pc-X @atom:* @atom:c @atom:pc @atom:* + @dihedral:X-c-pd-X @atom:* @atom:c @atom:pd @atom:* + @dihedral:X-c-pe-X @atom:* @atom:c @atom:pe @atom:* + @dihedral:X-c-pf-X @atom:* @atom:c @atom:pf @atom:* + @dihedral:X-c-p3-X @atom:* @atom:c @atom:p3 @atom:* + @dihedral:X-c-p4-X @atom:* @atom:c @atom:p4 @atom:* + @dihedral:X-c-px-X @atom:* @atom:c @atom:px @atom:* + @dihedral:X-c-p5-X @atom:* @atom:c @atom:p5 @atom:* + @dihedral:X-c-py-X @atom:* @atom:c @atom:py @atom:* + @dihedral:X-c-sh-X @atom:* @atom:c @atom:sh @atom:* + @dihedral:X-c-ss-X @atom:* @atom:c @atom:ss @atom:* + @dihedral:X-c-s4-X @atom:* @atom:c @atom:s4 @atom:* + @dihedral:X-c-sx-X @atom:* @atom:c @atom:sx @atom:* + @dihedral:X-c-s6-X @atom:* @atom:c @atom:s6 @atom:* + @dihedral:X-c-sy-X @atom:* @atom:c @atom:sy @atom:* + @dihedral:X-c1-c1-X @atom:* @atom:c1 @atom:c1 @atom:* + @dihedral:X-c1-cg-X @atom:* @atom:c1 @atom:cg @atom:* + @dihedral:X-c1-ch-X @atom:* @atom:c1 @atom:ch @atom:* + @dihedral:X-cg-cg-X @atom:* @atom:cg @atom:cg @atom:* + @dihedral:X-ch-ch-X @atom:* @atom:ch @atom:ch @atom:* + @dihedral:X-cg-ch-X @atom:* @atom:cg @atom:ch @atom:* + @dihedral:X-c1-c2-X @atom:* @atom:c1 @atom:c2 @atom:* + @dihedral:X-c1-c3-X @atom:* @atom:c1 @atom:c3 @atom:* + @dihedral:X-c1-ca-X @atom:* @atom:c1 @atom:ca @atom:* + @dihedral:X-c1-cc-X @atom:* @atom:c1 @atom:cc @atom:* + @dihedral:X-c1-cd-X @atom:* @atom:c1 @atom:cd @atom:* + @dihedral:X-c1-ce-X @atom:* @atom:c1 @atom:ce @atom:* + @dihedral:X-c1-cf-X @atom:* @atom:c1 @atom:cf @atom:* + @dihedral:X-c1-cu-X @atom:* @atom:c1 @atom:cu @atom:* + @dihedral:X-c1-cv-X @atom:* @atom:c1 @atom:cv @atom:* + @dihedral:X-c1-cx-X @atom:* @atom:c1 @atom:cx @atom:* + @dihedral:X-c1-cy-X @atom:* @atom:c1 @atom:cy @atom:* + @dihedral:X-c1-n-X @atom:* @atom:c1 @atom:n @atom:* + @dihedral:X-c1-n2-X @atom:* @atom:c1 @atom:n2 @atom:* + @dihedral:X-c1-n3-X @atom:* @atom:c1 @atom:n3 @atom:* + @dihedral:X-c1-n4-X @atom:* @atom:c1 @atom:n4 @atom:* + @dihedral:X-c1-na-X @atom:* @atom:c1 @atom:na @atom:* + @dihedral:X-c1-nb-X @atom:* @atom:c1 @atom:nb @atom:* + @dihedral:X-c1-nc-X @atom:* @atom:c1 @atom:nc @atom:* + @dihedral:X-c1-nd-X @atom:* @atom:c1 @atom:nd @atom:* + @dihedral:X-c1-ne-X @atom:* @atom:c1 @atom:ne @atom:* + @dihedral:X-c1-nf-X @atom:* @atom:c1 @atom:nf @atom:* + @dihedral:X-c1-nh-X @atom:* @atom:c1 @atom:nh @atom:* + @dihedral:X-c1-no-X @atom:* @atom:c1 @atom:no @atom:* + @dihedral:X-c1-oh-X @atom:* @atom:c1 @atom:oh @atom:* + @dihedral:X-c1-os-X @atom:* @atom:c1 @atom:os @atom:* + @dihedral:X-c1-p2-X @atom:* @atom:c1 @atom:p2 @atom:* + @dihedral:X-c1-pb-X @atom:* @atom:c1 @atom:pb @atom:* + @dihedral:X-c1-pc-X @atom:* @atom:c1 @atom:pc @atom:* + @dihedral:X-c1-pd-X @atom:* @atom:c1 @atom:pd @atom:* + @dihedral:X-c1-pe-X @atom:* @atom:c1 @atom:pe @atom:* + @dihedral:X-c1-pf-X @atom:* @atom:c1 @atom:pf @atom:* + @dihedral:X-c1-p3-X @atom:* @atom:c1 @atom:p3 @atom:* + @dihedral:X-c1-p4-X @atom:* @atom:c1 @atom:p4 @atom:* + @dihedral:X-c1-px-X @atom:* @atom:c1 @atom:px @atom:* + @dihedral:X-c1-p5-X @atom:* @atom:c1 @atom:p5 @atom:* + @dihedral:X-c1-py-X @atom:* @atom:c1 @atom:py @atom:* + @dihedral:X-c1-s2-X @atom:* @atom:c1 @atom:s2 @atom:* + @dihedral:X-c1-sh-X @atom:* @atom:c1 @atom:sh @atom:* + @dihedral:X-c1-ss-X @atom:* @atom:c1 @atom:ss @atom:* + @dihedral:X-c1-s4-X @atom:* @atom:c1 @atom:s4 @atom:* + @dihedral:X-c1-sx-X @atom:* @atom:c1 @atom:sx @atom:* + @dihedral:X-c1-s6-X @atom:* @atom:c1 @atom:s6 @atom:* + @dihedral:X-c1-sy-X @atom:* @atom:c1 @atom:sy @atom:* + @dihedral:X-c2-c2-X @atom:* @atom:c2 @atom:c2 @atom:* + @dihedral:X-c2-ce-X @atom:* @atom:c2 @atom:ce @atom:* + @dihedral:X-c2-cf-X @atom:* @atom:c2 @atom:cf @atom:* + @dihedral:X-ce-cf-X @atom:* @atom:ce @atom:cf @atom:* + @dihedral:X-ce-ce-X @atom:* @atom:ce @atom:ce @atom:* + @dihedral:X-cf-cf-X @atom:* @atom:cf @atom:cf @atom:* + @dihedral:X-cc-cd-X @atom:* @atom:cc @atom:cd @atom:* + @dihedral:X-cc-cc-X @atom:* @atom:cc @atom:cc @atom:* + @dihedral:X-cd-cd-X @atom:* @atom:cd @atom:cd @atom:* + @dihedral:X-c2-c3-X @atom:* @atom:c2 @atom:c3 @atom:* + @dihedral:X-c2-ca-X @atom:* @atom:c2 @atom:ca @atom:* + @dihedral:X-c2-n-X @atom:* @atom:c2 @atom:n @atom:* + @dihedral:X-c2-n2-X @atom:* @atom:c2 @atom:n2 @atom:* + @dihedral:X-c2-ne-X @atom:* @atom:c2 @atom:ne @atom:* + @dihedral:X-c2-nf-X @atom:* @atom:c2 @atom:nf @atom:* + @dihedral:X-ce-ne-X @atom:* @atom:ce @atom:ne @atom:* + @dihedral:X-cf-nf-X @atom:* @atom:cf @atom:nf @atom:* + @dihedral:X-c2-nc-X @atom:* @atom:c2 @atom:nc @atom:* + @dihedral:X-c2-nd-X @atom:* @atom:c2 @atom:nd @atom:* + @dihedral:X-cc-nd-X @atom:* @atom:cc @atom:nd @atom:* + @dihedral:X-cd-nc-X @atom:* @atom:cd @atom:nc @atom:* + @dihedral:X-cc-nc-X @atom:* @atom:cc @atom:nc @atom:* + @dihedral:X-cd-nd-X @atom:* @atom:cd @atom:nd @atom:* + @dihedral:X-c2-n3-X @atom:* @atom:c2 @atom:n3 @atom:* + @dihedral:X-c2-n4-X @atom:* @atom:c2 @atom:n4 @atom:* + @dihedral:X-c2-na-X @atom:* @atom:c2 @atom:na @atom:* + @dihedral:X-cc-na-X @atom:* @atom:cc @atom:na @atom:* + @dihedral:X-cd-na-X @atom:* @atom:cd @atom:na @atom:* + @dihedral:X-c2-nh-X @atom:* @atom:c2 @atom:nh @atom:* + @dihedral:X-c2-no-X @atom:* @atom:c2 @atom:no @atom:* + @dihedral:X-c2-oh-X @atom:* @atom:c2 @atom:oh @atom:* + @dihedral:X-c2-os-X @atom:* @atom:c2 @atom:os @atom:* + @dihedral:X-c2-p2-X @atom:* @atom:c2 @atom:p2 @atom:* + @dihedral:X-c2-pe-X @atom:* @atom:c2 @atom:pe @atom:* + @dihedral:X-c2-pf-X @atom:* @atom:c2 @atom:pf @atom:* + @dihedral:X-ce-pf-X @atom:* @atom:ce @atom:pf @atom:* + @dihedral:X-ce-pe-X @atom:* @atom:ce @atom:pe @atom:* + @dihedral:X-cf-pf-X @atom:* @atom:cf @atom:pf @atom:* + @dihedral:X-c2-pc-X @atom:* @atom:c2 @atom:pc @atom:* + @dihedral:X-c2-pd-X @atom:* @atom:c2 @atom:pd @atom:* + @dihedral:X-cc-pc-X @atom:* @atom:cc @atom:pc @atom:* + @dihedral:X-cc-pd-X @atom:* @atom:cc @atom:pd @atom:* + @dihedral:X-cd-pc-X @atom:* @atom:cd @atom:pc @atom:* + @dihedral:X-cd-pd-X @atom:* @atom:cd @atom:pd @atom:* + @dihedral:X-c2-p3-X @atom:* @atom:c2 @atom:p3 @atom:* + @dihedral:X-c2-p4-X @atom:* @atom:c2 @atom:p4 @atom:* + @dihedral:X-ce-p4-X @atom:* @atom:ce @atom:p4 @atom:* + @dihedral:X-cf-p4-X @atom:* @atom:cf @atom:p4 @atom:* + @dihedral:X-c2-px-X @atom:* @atom:c2 @atom:px @atom:* + @dihedral:X-ce-px-X @atom:* @atom:ce @atom:px @atom:* + @dihedral:X-cf-px-X @atom:* @atom:cf @atom:px @atom:* + @dihedral:X-c2-p5-X @atom:* @atom:c2 @atom:p5 @atom:* + @dihedral:X-ce-p5-X @atom:* @atom:ce @atom:p5 @atom:* + @dihedral:X-cf-p5-X @atom:* @atom:cf @atom:p5 @atom:* + @dihedral:X-c2-py-X @atom:* @atom:c2 @atom:py @atom:* + @dihedral:X-ce-py-X @atom:* @atom:ce @atom:py @atom:* + @dihedral:X-cf-py-X @atom:* @atom:cf @atom:py @atom:* + @dihedral:X-c2-sh-X @atom:* @atom:c2 @atom:sh @atom:* + @dihedral:X-c2-ss-X @atom:* @atom:c2 @atom:ss @atom:* + @dihedral:X-c2-s4-X @atom:* @atom:c2 @atom:s4 @atom:* + @dihedral:X-ce-s4-X @atom:* @atom:ce @atom:s4 @atom:* + @dihedral:X-cf-s4-X @atom:* @atom:cf @atom:s4 @atom:* + @dihedral:X-c2-sx-X @atom:* @atom:c2 @atom:sx @atom:* + @dihedral:X-ce-sx-X @atom:* @atom:ce @atom:sx @atom:* + @dihedral:X-cf-sx-X @atom:* @atom:cf @atom:sx @atom:* + @dihedral:X-c2-s6-X @atom:* @atom:c2 @atom:s6 @atom:* + @dihedral:X-ce-s6-X @atom:* @atom:ce @atom:s6 @atom:* + @dihedral:X-cf-s6-X @atom:* @atom:cf @atom:s6 @atom:* + @dihedral:X-c2-sy-X @atom:* @atom:c2 @atom:sy @atom:* + @dihedral:X-ce-sy-X @atom:* @atom:ce @atom:sy @atom:* + @dihedral:X-cf-sy-X @atom:* @atom:cf @atom:sy @atom:* + @dihedral:X-c3-c3-X @atom:* @atom:c3 @atom:c3 @atom:* + @dihedral:X-cx-cx-X @atom:* @atom:cx @atom:cx @atom:* + @dihedral:X-cy-cy-X @atom:* @atom:cy @atom:cy @atom:* + @dihedral:X-c3-ca-X @atom:* @atom:c3 @atom:ca @atom:* + @dihedral:X-c3-n-X @atom:* @atom:c3 @atom:n @atom:* + @dihedral:X-cx-n-X @atom:* @atom:cx @atom:n @atom:* + @dihedral:X-cy-n-X @atom:* @atom:cy @atom:n @atom:* + @dihedral:X-c3-n2-X @atom:* @atom:c3 @atom:n2 @atom:* + @dihedral:X-c3-ne-X @atom:* @atom:c3 @atom:ne @atom:* + @dihedral:X-c3-nf-X @atom:* @atom:c3 @atom:nf @atom:* + @dihedral:X-c3-n3-X @atom:* @atom:c3 @atom:n3 @atom:* + @dihedral:X-c3-n4-X @atom:* @atom:c3 @atom:n4 @atom:* + @dihedral:X-c3-na-X @atom:* @atom:c3 @atom:na @atom:* + @dihedral:X-c3-nh-X @atom:* @atom:c3 @atom:nh @atom:* + @dihedral:X-c3-no-X @atom:* @atom:c3 @atom:no @atom:* + @dihedral:X-c3-oh-X @atom:* @atom:c3 @atom:oh @atom:* + @dihedral:X-c3-os-X @atom:* @atom:c3 @atom:os @atom:* + @dihedral:X-c3-p2-X @atom:* 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@dihedral:oh-p5-os-c3 @atom:oh @atom:p5 @atom:os @atom:c3 + @dihedral:oh-p5-os-c3 @atom:oh @atom:p5 @atom:os @atom:c3 + @dihedral:os-p5-os-c3 @atom:os @atom:p5 @atom:os @atom:c3 + @dihedral:os-p5-os-c3 @atom:os @atom:p5 @atom:os @atom:c3 + @dihedral:h1-c3-c-o @atom:h1 @atom:c3 @atom:c @atom:o + @dihedral:h1-c3-c-o @atom:h1 @atom:c3 @atom:c @atom:o + @dihedral:hc-c3-c-o @atom:hc @atom:c3 @atom:c @atom:o + @dihedral:hc-c3-c-o @atom:hc @atom:c3 @atom:c @atom:o + @dihedral:hc-c3-c3-hc @atom:hc @atom:c3 @atom:c3 @atom:hc + @dihedral:hc-c3-c3-c3 @atom:hc @atom:c3 @atom:c3 @atom:c3 + @dihedral:hc-c3-c2-c2 @atom:hc @atom:c3 @atom:c2 @atom:c2 + @dihedral:hc-c3-c2-c2 @atom:hc @atom:c3 @atom:c2 @atom:c2 + @dihedral:ho-oh-c3-c3 @atom:ho @atom:oh @atom:c3 @atom:c3 + @dihedral:ho-oh-c3-c3 @atom:ho @atom:oh @atom:c3 @atom:c3 + @dihedral:ho-oh-c-o @atom:ho @atom:oh @atom:c @atom:o + @dihedral:ho-oh-c-o @atom:ho @atom:oh @atom:c @atom:o + @dihedral:c2-c2-c-o @atom:c2 @atom:c2 @atom:c @atom:o + @dihedral:c2-c2-c-o @atom:c2 @atom:c2 @atom:c @atom:o + @dihedral:c3-c2-c2-c3 @atom:c3 @atom:c2 @atom:c2 @atom:c3 + @dihedral:c3-c2-c2-c3 @atom:c3 @atom:c2 @atom:c2 @atom:c3 + @dihedral:c3-c3-c3-c3 @atom:c3 @atom:c3 @atom:c3 @atom:c3 + @dihedral:c3-c3-c3-c3 @atom:c3 @atom:c3 @atom:c3 @atom:c3 + @dihedral:c3-c3-c3-c3 @atom:c3 @atom:c3 @atom:c3 @atom:c3 + @dihedral:c3-c3-n3-c3 @atom:c3 @atom:c3 @atom:n3 @atom:c3 + @dihedral:c3-c3-n3-c3 @atom:c3 @atom:c3 @atom:n3 @atom:c3 + @dihedral:c3-c3-os-c3 @atom:c3 @atom:c3 @atom:os @atom:c3 + @dihedral:c3-c3-os-c3 @atom:c3 @atom:c3 @atom:os @atom:c3 + @dihedral:c3-c3-os-c @atom:c3 @atom:c3 @atom:os @atom:c + @dihedral:c3-c3-os-c @atom:c3 @atom:c3 @atom:os @atom:c + @dihedral:c3-os-c3-os @atom:c3 @atom:os @atom:c3 @atom:os + @dihedral:c3-os-c3-os @atom:c3 @atom:os @atom:c3 @atom:os + @dihedral:c3-os-c3-os @atom:c3 @atom:os @atom:c3 @atom:os + @dihedral:c3-os-c3-na @atom:c3 @atom:os @atom:c3 @atom:na + @dihedral:c3-os-c3-na @atom:c3 @atom:os @atom:c3 @atom:na + @dihedral:o-c-os-c3 @atom:o @atom:c @atom:os @atom:c3 + @dihedral:o-c-os-c3 @atom:o @atom:c @atom:os @atom:c3 + @dihedral:os-c3-na-c2 @atom:os @atom:c3 @atom:na @atom:c2 + @dihedral:os-c3-na-c2 @atom:os @atom:c3 @atom:na @atom:c2 + @dihedral:os-c3-c3-os @atom:os @atom:c3 @atom:c3 @atom:os + @dihedral:os-c3-c3-os @atom:os @atom:c3 @atom:c3 @atom:os + @dihedral:os-c3-c3-oh @atom:os @atom:c3 @atom:c3 @atom:oh + @dihedral:os-c3-c3-oh @atom:os @atom:c3 @atom:c3 @atom:oh + @dihedral:oh-c3-c3-oh @atom:oh @atom:c3 @atom:c3 @atom:oh + @dihedral:oh-c3-c3-oh @atom:oh @atom:c3 @atom:c3 @atom:oh + @dihedral:f-c3-c3-f @atom:f @atom:c3 @atom:c3 @atom:f + @dihedral:f-c3-c3-f @atom:f @atom:c3 @atom:c3 @atom:f + @dihedral:cl-c3-c3-cl @atom:cl @atom:c3 @atom:c3 @atom:cl + @dihedral:cl-c3-c3-cl @atom:cl @atom:c3 @atom:c3 @atom:cl + @dihedral:br-c3-c3-br @atom:br @atom:c3 @atom:c3 @atom:br + @dihedral:br-c3-c3-br @atom:br @atom:c3 @atom:c3 @atom:br + @dihedral:h1-c3-c3-os @atom:h1 @atom:c3 @atom:c3 @atom:os + @dihedral:h1-c3-c3-os @atom:h1 @atom:c3 @atom:c3 @atom:os + @dihedral:h1-c3-c3-oh @atom:h1 @atom:c3 @atom:c3 @atom:oh + @dihedral:h1-c3-c3-oh @atom:h1 @atom:c3 @atom:c3 @atom:oh + @dihedral:h1-c3-c3-f @atom:h1 @atom:c3 @atom:c3 @atom:f + @dihedral:h1-c3-c3-f @atom:h1 @atom:c3 @atom:c3 @atom:f + @dihedral:h1-c3-c3-cl @atom:h1 @atom:c3 @atom:c3 @atom:cl + @dihedral:h1-c3-c3-cl @atom:h1 @atom:c3 @atom:c3 @atom:cl + @dihedral:h1-c3-c3-br @atom:h1 @atom:c3 @atom:c3 @atom:br + @dihedral:h1-c3-c3-br @atom:h1 @atom:c3 @atom:c3 @atom:br + @dihedral:hc-c3-c3-os @atom:hc @atom:c3 @atom:c3 @atom:os + @dihedral:hc-c3-c3-os @atom:hc @atom:c3 @atom:c3 @atom:os + @dihedral:hc-c3-c3-oh @atom:hc @atom:c3 @atom:c3 @atom:oh + @dihedral:hc-c3-c3-oh @atom:hc @atom:c3 @atom:c3 @atom:oh + @dihedral:hc-c3-c3-f @atom:hc @atom:c3 @atom:c3 @atom:f + @dihedral:hc-c3-c3-f @atom:hc @atom:c3 @atom:c3 @atom:f + @dihedral:hc-c3-c3-cl @atom:hc @atom:c3 @atom:c3 @atom:cl + @dihedral:hc-c3-c3-cl @atom:hc @atom:c3 @atom:c3 @atom:cl + @dihedral:hc-c3-c3-br @atom:hc @atom:c3 @atom:c3 @atom:br + @dihedral:hc-c3-c3-br @atom:hc @atom:c3 @atom:c3 @atom:br + } # (end of Dihedrals By Type) + + write_once("In Settings") { + improper_coeff @improper:X-o-c-o cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:X-X-c-o cvff 10.5 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:X-X-ca-ha cvff 1.1 -1 2 # bsd.on C6H6 nmodes + improper_coeff @improper:X-X-n-hn cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:X-X-n2-hn cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:X-X-na-hn cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:X-c3-n-c3 cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:X-n2-ca-n2 cvff 10.5 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:c-c2-c2-c3 cvff 1.1 -1 2 # dac guess, 9/94 + improper_coeff @improper:c-ca-ca-c3 cvff 1.1 -1 2 # dac guess, 9/94 + improper_coeff @improper:c-c3-n-hn cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:c-c3-n-o cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:c2-c2-na-c3 cvff 1.1 -1 2 # + improper_coeff @improper:c2-c-c2-c3 cvff 1.1 -1 2 # + improper_coeff @improper:c2-c3-c2-hc cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:c2-c3-ca-hc cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:c2-hc-c-o cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:c3-o-c-oh cvff 1.1 -1 2 # + improper_coeff @improper:c3-c2-c2-n2 cvff 1.1 -1 2 # + improper_coeff @improper:c3-c2-c2-na cvff 1.1 -1 2 # + improper_coeff @improper:c3-ca-ca-n2 cvff 1.1 -1 2 # + improper_coeff @improper:c3-ca-ca-na cvff 1.1 -1 2 # + improper_coeff @improper:ca-ca-ca-c2 cvff 1.1 -1 2 # + improper_coeff @improper:ca-ca-ca-c3 cvff 1.1 -1 2 # + improper_coeff @improper:ca-ca-ca-f cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-ca-ca-cl cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-ca-ca-br cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-ca-ca-i cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-ca-c-oh cvff 1.1 -1 2 # (not used in tyr!) + improper_coeff @improper:ca-ca-na-c3 cvff 1.1 -1 2 # + improper_coeff @improper:ca-c-ca-c3 cvff 1.1 -1 2 # + improper_coeff @improper:ca-hc-c-o cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-n2-ca-n2 cvff 1.1 -1 2 # dac, 10/94 + improper_coeff @improper:hc-o-c-oh cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:hc-o-c-os cvff 1.1 -1 2 # + improper_coeff @improper:n2-c2-ca-n2 cvff 1.1 -1 2 # dac guess, 9/94 + improper_coeff @improper:n2-ca-ca-n2 cvff 1.1 -1 2 # dac guess, 9/94 + improper_coeff @improper:na-n2-ca-n2 cvff 1.1 -1 2 # dac, 10/94 + } # (end of improper_coeffs) + + write_once("Data Impropers By Type") { + @improper:X-o-c-o @atom:* @atom:o @atom:c @atom:o + @improper:X-X-c-o @atom:* @atom:* @atom:c @atom:o + @improper:X-X-ca-ha @atom:* @atom:* @atom:ca @atom:ha + @improper:X-X-n-hn @atom:* @atom:* @atom:n @atom:hn + @improper:X-X-n2-hn @atom:* @atom:* @atom:n2 @atom:hn + @improper:X-X-na-hn @atom:* @atom:* @atom:na @atom:hn + @improper:X-c3-n-c3 @atom:* @atom:c3 @atom:n @atom:c3 + @improper:X-n2-ca-n2 @atom:* @atom:n2 @atom:ca @atom:n2 + @improper:c-c2-c2-c3 @atom:c @atom:c2 @atom:c2 @atom:c3 + @improper:c-ca-ca-c3 @atom:c @atom:ca @atom:ca @atom:c3 + @improper:c-c3-n-hn @atom:c @atom:c3 @atom:n @atom:hn + @improper:c-c3-n-o @atom:c @atom:c3 @atom:n @atom:o + @improper:c2-c2-na-c3 @atom:c2 @atom:c2 @atom:na @atom:c3 + @improper:c2-c-c2-c3 @atom:c2 @atom:c @atom:c2 @atom:c3 + @improper:c2-c3-c2-hc @atom:c2 @atom:c3 @atom:c2 @atom:hc + @improper:c2-c3-ca-hc @atom:c2 @atom:c3 @atom:ca @atom:hc + @improper:c2-hc-c-o @atom:c2 @atom:hc @atom:c @atom:o + @improper:c3-o-c-oh @atom:c3 @atom:o @atom:c @atom:oh + @improper:c3-c2-c2-n2 @atom:c3 @atom:c2 @atom:c2 @atom:n2 + @improper:c3-c2-c2-na @atom:c3 @atom:c2 @atom:c2 @atom:na + @improper:c3-ca-ca-n2 @atom:c3 @atom:ca @atom:ca @atom:n2 + @improper:c3-ca-ca-na @atom:c3 @atom:ca @atom:ca @atom:na + @improper:ca-ca-ca-c2 @atom:ca @atom:ca @atom:ca @atom:c2 + @improper:ca-ca-ca-c3 @atom:ca @atom:ca @atom:ca @atom:c3 + @improper:ca-ca-ca-f @atom:ca @atom:ca @atom:ca @atom:f + @improper:ca-ca-ca-cl @atom:ca @atom:ca @atom:ca @atom:cl + @improper:ca-ca-ca-br @atom:ca @atom:ca @atom:ca @atom:br + @improper:ca-ca-ca-i @atom:ca @atom:ca @atom:ca @atom:i + @improper:ca-ca-c-oh @atom:ca @atom:ca @atom:c @atom:oh + @improper:ca-ca-na-c3 @atom:ca @atom:ca @atom:na @atom:c3 + @improper:ca-c-ca-c3 @atom:ca @atom:c @atom:ca @atom:c3 + @improper:ca-hc-c-o @atom:ca @atom:hc @atom:c @atom:o + @improper:ca-n2-ca-n2 @atom:ca @atom:n2 @atom:ca @atom:n2 + @improper:hc-o-c-oh @atom:hc @atom:o @atom:c @atom:oh + @improper:hc-o-c-os @atom:hc @atom:o @atom:c @atom:os + @improper:n2-c2-ca-n2 @atom:n2 @atom:c2 @atom:ca @atom:n2 + @improper:n2-ca-ca-n2 @atom:n2 @atom:ca @atom:ca @atom:n2 + @improper:na-n2-ca-n2 @atom:na @atom:n2 @atom:ca @atom:n2 + } # (end of Impropers By Type) + + + write_once("In Init") { + # Default styles and settings for AMBER based force-fields: + units real + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid fourier + improper_style hybrid cvff + pair_style hybrid lj/charmm/coul/charmm 9.0 10.0 + + # NOTE: Long-range coulombic forces were disabled intentionally. (See below) + # If you want to use long-range electrostatics, uncomment these lines: + # + #pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + #kspace_style pppm 0.0001 + # + # Instead I use hybrid lj/charmm/coul/charmm by default, because + # LAMMPS complains if you attempt to use lj/charmm/coul/long on a + # system if it does not contain any charged particles. + # Currently, moltemplate does not assign atomic charge, + # so this problem occurs frequently. + + pair_modify mix arithmetic + special_bonds amber + } + +} + + diff --git a/tools/moltemplate/common/graphene.lt b/tools/moltemplate/common/graphene.lt new file mode 100644 index 000000000..4a17862fc --- /dev/null +++ b/tools/moltemplate/common/graphene.lt @@ -0,0 +1,106 @@ +# This file contains a unit cell for building graphene and nanotubes +# +# +# The 2AtomCellAlignX "molecule" defined below is a minimal unit cell for any +# hexagonal tesselation in 2-dimensions. (See "graphene_unit_cell.jpg") +# Surfaces constructed with this unit cell can be flat or curved into tubes. +# The distance between nearest-neighbor carbon atoms (ie the length of a +# carbon-carbon bond) is equal to "d" which I set to 1.420 Angstroms. +# +# d = length of each hexagon's side = 1.42 Angstroms +# L = length of each hexagon = 2*d = 2.84 Angstroms +# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478056 Angstroms +# +# Consequently, the Lattice-cell vectors for singe-layer graphene are: +# (2.4595121467478, 0, 0) (aligned with X axis) +# (1.2297560733739, 2.13, 0) (2.13 = 1.5*d) +# So, to build a sheet of graphite, you could use: +# sheet = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) + + + + +Graphene { + + 2AtomCellAlignX + { + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0 + $atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0 + } + } + + # Now define properties of the Carbon graphene atom + + write_once("In Init") { + pair_style hybrid lj/charmm/coul/charmm 9.0 10.0 + } + + write_once("Data Masses") { + @atom:C 12.0 + } + + write_once("In Settings") { + # i j epsilon sigma + pair_coeff @atom:C @atom:C lj/charmm/coul/charmm 0.068443 3.407 + + # These Lennard-Jones parameters come from + # R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus, + # Chem Phys Lett, 348:187 (2001) + + # Define a group consisting of only carbon atoms in graphene molecules + group Cgraphene type @atom:C + } + + # Notice that the two atoms in the unit-cell above lie in the XY plane. + # (Their z-coordinate is zero). It's also useful to have a version of + # this object which lies in the XZ plan. So we define this below: + + 2AtomCellAlignXZ = 2AtomCellAlignX.rot(90,1,0,0) + +} # Graphene + + + + + + + + + + +# ------------ Graphite ----------- +# +# Note: For graphite: sheets stacked in the Z direction are separated by a +# distance of 3.35 Angstroms, and shifted in an alternating +/-Y direction +# by a distance of d (1.42 Angstroms). To add additional graphene layers +# you could use: +# sheet2 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) +# sheet2[*][*].move(0, 1.42, 3.35) +# sheet3 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) +# sheet3[*][*].move(0, -1.42, 6.70) +# etc... +# However, to build a thick sheet of graphite, it would +# be more efficient to use a 4-atom unit cell: +# +#Graphene { +# GraphiteCell { +# # atomID molID atomType charge x y z +# write("Data Atoms") { +# $atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0 +# $atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0 +# $atom:C3 $mol:... @atom:../C 0.0 -0.61487803668695 1.065 3.35 +# $atom:C4 $mol:... @atom:../C 0.0 0.61487803668695 1.775 3.35 +# } +# } # GraphiteCell +#} +# +# Then you could create a thick sheet of graphite this way: +# +# graphite = new Graphene/GraphiteCell [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) +# [5].move(0,0,6.70) diff --git a/tools/moltemplate/common/images/graphene_unit_cell.jpg b/tools/moltemplate/common/images/graphene_unit_cell.jpg new file mode 100644 index 000000000..12dbf8fca Binary files /dev/null and b/tools/moltemplate/common/images/graphene_unit_cell.jpg differ diff --git a/tools/moltemplate/common/images/ice_rect8_unitcell.png b/tools/moltemplate/common/images/ice_rect8_unitcell.png new file mode 100644 index 000000000..5bd6057e1 Binary files /dev/null and b/tools/moltemplate/common/images/ice_rect8_unitcell.png differ diff --git a/tools/moltemplate/common/images/spce_ball_and_stick.jpg b/tools/moltemplate/common/images/spce_ball_and_stick.jpg new file mode 100644 index 000000000..60aaf90b9 Binary files /dev/null and b/tools/moltemplate/common/images/spce_ball_and_stick.jpg differ diff --git a/tools/moltemplate/common/spce.lt b/tools/moltemplate/common/spce.lt new file mode 100644 index 000000000..019911c19 --- /dev/null +++ b/tools/moltemplate/common/spce.lt @@ -0,0 +1,52 @@ +# file "spce.lt" +# +# H1 H2 +# \ / +# O + +SPCE { + + write_once("In Init") { + # -- Default styles (for solo "SPCE" water) -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 + $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 + } + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 1000.0 1.0 + angle_coeff @angle:HOH harmonic 1000.0 109.47 + pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + group spce type @atom:O @atom:H + fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fShakeSPCE during minimization.) + } + +} # end of definition of "SPCE" water molecule type + diff --git a/tools/moltemplate/common/spce_ice_rect8.lt b/tools/moltemplate/common/spce_ice_rect8.lt new file mode 100644 index 000000000..ccfd2f18c --- /dev/null +++ b/tools/moltemplate/common/spce_ice_rect8.lt @@ -0,0 +1,57 @@ +# This ice (1h) unit cell is rectangular and contains 8 water molecules. +# (Coordinates and cell dimensions converted were from a PDB file.) +# The dimensions of the unit cell (in Angstroms) are: 4.521 7.832 7.362 + + +import "spce.lt" # <-- define the "SPCE" molecule + +SpceIceRect8 { + + # Create a 3-dimensional array of 8 water molecules + + wat = new SPCE[2][2][2] + + # Array indices will be correlated with position [xindex][yindex][zindex] + + # You can overwrite coordinates of atoms after they were created this way: + # (Order is not important) + # atom-ID molecule-ID atomType charge newX newY newZ + + write("Data Atoms") { + $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381 + $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 0.370 1.710 + $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.710 + $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981 + $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 1.305 6.970 + $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.652 + $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300 + $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 2.611 3.289 + $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.320 2.143 1.971 + $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061 + $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.143 5.391 + $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 3.546 5.391 + $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381 + $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 4.286 1.710 + $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 0.320 5.688 1.710 + $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981 + $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 5.221 6.970 + $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.940 5.688 5.652 + $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300 + $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.289 + $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 2.582 6.058 1.971 + $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061 + $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 4.200 6.058 5.391 + $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.462 5.391 + } +} # IceRect8 + +# Credit goes to Martin Chaplin. +# These coordinates were orignally downloaded from Martin Chaplin's +# website: http://www.btinternet.com/~martin.chaplin/ice1h.html +# ... and then they were stretched independently in the xy and z +# directions in order to match the lattice parameters measured by +# Rottger et al., +# "Lattice constants and thermal expansion of H2O and D2O ice Ih" +# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648 +# I am using the lattice constants measured at temperature 265K +# (and pressure=100Torr). diff --git a/tools/moltemplate/common/tip3p_1983.lt b/tools/moltemplate/common/tip3p_1983.lt new file mode 100644 index 000000000..45dc4ee9d --- /dev/null +++ b/tools/moltemplate/common/tip3p_1983.lt @@ -0,0 +1,123 @@ +############################################################# +# WARNING: THIS FILE HAS NOT BEEN TESTED! +# (If you use this file in a simulation, please email me to let me know +# if it worked. -Andrew 2012-10, (jewett dot aij at gmail dot com)) +######################################################### +# There are two different versions of TIP3P: +# +# tip3p_1983.lt # The implementation of TIP3P used by CHARMM (I think). +# tip3p_2004.lt # The newer Price & Brooks, J. Chem Phys 2004 model +# # which uses long-range coulombics +######################################################### + +# file "tip3p_1983.lt" +# +# H1 H2 +# \ / +# O +# +# I think this is the TIP3P water model used by CHARMM (and AMBER?). See: +# Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983) + + +TIP3P_1983 { + + write_once("In Init") { + # -- Default styles (for solo "TIP3P_1983" water) -- + units real + atom_style full + + # I'm not sure exactly which cutoffs distances are traditionally used in + # in the 1983 "TIP3P" model by Jorgensen model, (used by CHARMM). + # (See the Price JCP 2004 paper for a review.) + # My first guess was this: + # pair_style hybrid lj/charmm/coul/charmm 7.5 8.0 10.0 10.5 + # However, in the LAMMPS "peptide" example, they use these parameters: + + pair_style hybrid lj/charmm/coul/long 8.0 10.0 10.0 + + # ...alternately, if this does not work, try this: + # pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.0 10.5 + + bond_style hybrid harmonic + angle_style hybrid harmonic + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:O -0.834 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:H 0.417 0.756950327 0.00000 0.5858822766 + $atom:H2 $mol:. @atom:H 0.417 -0.756950327 0.00000 0.5858822766 + } + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 450.0 0.9572 + angle_coeff @angle:HOH harmonic 55.0 104.52 + + ######################################################################### + #### There are two choices for for the O-O interactions + ######################################################################### + #### O-O nonbonded interactions + # For the 1983 Jorgensen version of TIP3P use: + + pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.1521 3.1507 + + # For the 2004 Price & Brooks version of TIP3P use: + # pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.102 3.188 + ######################################################################### + #### There are three choices for for the O-H and H-H interactions + ######################################################################### + #### 1) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter + + pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000 + pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.7753 #arithmetic + + ######################################################################### + #### 2) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter, + #### If you want to use this, uncomment the following two lines: + # pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000 + # pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.1226 #geometric + ######################################################################### + #### 3) The original Jorgensen 1983 parameterization has no OH or HH + # lennard-jones interactions. (?? I think ??) + # For this behavior, uncomment these lines: + # pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.00 0.4000 + # pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.00 1.7753 + ######################################################################### + + # Define a group for the tip3p water molecules: + group tip3p type @atom:O @atom:H + + # Optional: Constrain the angles and distances. + # (Most implementations use this, but it is optional.) + fix fShakeTIP3P tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fShakeTIP3P during minimization.) + } + +} # "TIP3P_1983" water molecule type + + + + +# (note to self:) +# In the LAMMPS "peptide" example, these (nearly identical) parameters were used +# and they left the O-H parameters to be determined by the default mixing rules +#pair_style lj/charmm/coul/long 8.0 10.0 10.0 +#pair_coeff @atom:H @atom:H 0.046 0.400014 0.046 0.400014 +#pair_coeff @atom:O @atom:O 0.1521 3.15057 0.1521 3.15057 +#angle_style charmm +#angle_coeff @angle:HOH 55.0 104.52 0.0 0.0 diff --git a/tools/moltemplate/common/tip3p_2004.lt b/tools/moltemplate/common/tip3p_2004.lt new file mode 100644 index 000000000..06964c7b6 --- /dev/null +++ b/tools/moltemplate/common/tip3p_2004.lt @@ -0,0 +1,97 @@ +######################################################### +# Warning: This file has not been carefully tested. +######################################################### +# There are two different versions of TIP3P: +# +# tip3p_1983.lt # The implementation of TIP3P used by CHARMM (I think). +# tip3p_2004.lt # The newer Price & Brooks, J. Chem Phys 2004 model +# # which uses long-range coulombics +######################################################### + +# file "tip3p_2004.lt" +# +# H1 H2 +# \ / +# O +# +# I think this is the TIP3P water described in the paper by +# Daniel J. Price and Charles L. Brooks III +# J. Chem. Phys., 121(20): 10096 (2004) +# Specifically I think it refers to the "Model B" version of long-range TIP3P +# described in the 3rd-to-last column of "Table I", on p.10099. + +TIP3P_2004 { + + write_once("In Init") { + # -- Default styles (for solo "TIP3P_2004" water) -- + units real + atom_style full + + pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.5 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:ow -0.830 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:hw 0.415 0.756950327 0.00000 0.5858822766 + $atom:H2 $mol:. @atom:hw 0.415 -0.756950327 0.00000 0.5858822766 + } + + write_once("Data Masses") { + @atom:ow 15.9994 + @atom:hw 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 450.0 0.9572 + angle_coeff @angle:HOH harmonic 55.0 104.52 + + ######################################################################### + #### There are two choices for for the O-O interactions + ######################################################################### + #### O-O nonbonded interactions + # For the 1983 Jorgensen version of TIP3P use: + # pair_coeff @atom:ow @atom:ow lj/charmm/coul/charmm 0.1521 3.1507 + # For the 2004 Price & Brooks version of TIP3P use: + pair_coeff @atom:ow @atom:ow lj/charmm/coul/long 0.102 3.188 + ######################################################################### + #### There are three choices for for the O-H and H-H interactions + ######################################################################### + #### 1) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter + pair_coeff @atom:hw @atom:hw lj/charmm/coul/long 0.0460 0.4000 + pair_coeff @atom:ow @atom:hw lj/charmm/coul/long 0.0836 1.7753 #arithmetic + ######################################################################### + #### 2) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter, + #### If you want to use this, uncomment the following two lines: + # pair_coeff @atom:hw @atom:hw lj/charmm/coul/charmm 0.0460 0.4000 + # pair_coeff @atom:ow @atom:hw lj/charmm/coul/charmm 0.0836 1.1226 #geometric + ######################################################################### + #### 3) The original Jorgensen 1983 parameterization has no OH or HH + # lennard-jones interactions. For this behavior, uncomment these lines: + # pair_coeff @atom:hw @atom:hw lj/charmm/coul/charmm 0.00 0.4000 + # pair_coeff @atom:ow @atom:hw lj/charmm/coul/charmm 0.00 1.7753 + ######################################################################### + + # Define a group for the tip3p water molecules: + group tip3p type @atom:ow @atom:hw + + # Optional: Constrain the angles and distances. + # (Most implementations use this, but it is optional.) + fix fShakeTIP3P tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fShakeTIP3P during minimization.) + } + +} # "TIP3P_2004" water molecule type + diff --git a/tools/moltemplate/common/trappe1998.lt b/tools/moltemplate/common/trappe1998.lt new file mode 100644 index 000000000..9bcc80cb1 --- /dev/null +++ b/tools/moltemplate/common/trappe1998.lt @@ -0,0 +1,50 @@ +# This file stores complete LAMMPS data for the TraPPE model of saturated +# hydrocarbon chains. In this "united-atom" model, each methyl group is +# represented by a single atom. Forces between "atoms" are taken from the +# TraPPE force-field. (J Phys Chem B, 1998, volume 102, pp.2569-2577) + +TraPPE { + + write_once("In Init") { + # -- Default styles for "TraPPE" -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid opls + improper_style none + pair_style hybrid lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:CH2 14.1707 + @atom:CH3 15.2507 + @atom:CH4 16.3307 + } + + write_once("Data Angles By Type") { + @angle:backbone @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated + } + + write_once("Data Dihedrals By Type") { + @dihedral:backbone @atom:CH? @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated @bond:saturated + } + + write_once("In Settings") { + pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95 + pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75 + pair_coeff @atom:CH4 @atom:CH4 lj/charmm/coul/charmm 0.294106636 3.73 + bond_coeff @bond:saturated harmonic 120.0 1.54 + angle_coeff @angle:backbone harmonic 62.0022 114 + dihedral_coeff @dihedral:backbone opls 1.411036 -0.271016 3.145034 0.0 + } + + write_once("In Settings") { + group TraPPE type @atom:CH2 @atom:CH3 @atom:CH4 + } + +} # class TraPPE + diff --git a/tools/moltemplate/common/watmw.lt b/tools/moltemplate/common/watmw.lt new file mode 100644 index 000000000..c7aaecebb --- /dev/null +++ b/tools/moltemplate/common/watmw.lt @@ -0,0 +1,54 @@ +# This file stores LAMMPS data for the "mW" water model. +# (Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016) +# +# In this model, each water molecule is represented by a single "mW" particle. +# These particles interact with their neighbors via 3-body Stillinger-Weber +# forces whose parameters are tuned to mimic directional hydrogen-bonding +# in liquid water (as well as hexagonal ice, type II ice, and +# low-density super-cooled liquid/amorphous water phases). + +WatMW { + write("Data Atoms") { + $atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:mW 18.02 + } + + write_once("system.in.sw") { + mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.333333333 7.049556277 0.602224558 4 0 0 + } + + write_once("In Init") { + # -- Default styles for "WatMW" -- + units real + pair_style sw + } + + write_once("In Settings") { + # --Now indicate which atom type(s) are simulated using the "sw" pair style + # -- In this case only one of the atom types is used (the mW water "atom"). + + pair_coeff * * sw system.in.sw mW NULL NULL NULL + + # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so + # -- the atoms are identified by order in the list, not by name. (The "mW" + # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) + # -- This command says that the first atom type corresponds to the "mW" + # -- atom in system.in.sw, and to ignore the remaining three atom types + # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. + # -- We don't want to use the "sw" force field for interactions involving + # -- these atom types, so we put "NULL" there.) + # -- Note: For this to work, you should probably run moltemplate this way: + # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt + # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom) + } + + # -- optional -- + + write_once("In Settings") { + group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group) + } + +} # WatMW diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README.TXT b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README.TXT new file mode 100644 index 000000000..09abbc4b2 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README.TXT @@ -0,0 +1,70 @@ + This example shows how to put a protein (inclusion) in a + lipid bilayer mixture composed of two different lipids (DPPC and DLPC). + The DPPC lipid model is described here: + G. Brannigan, P.F. Philips, and F.L.H. Brown, + Physical Review E, Vol 72, 011915 (2005) + (The DLPC model is a truncated version of DPPC. Modifications discussed below.) + The protein model is described here: + G. Bellesia, AI Jewett, and J-E Shea, + Protein Science, Vol19 141-154 (2010) + +--- PREREQUISITES: --- + +1) This example requires the "dihedral_style fourier", which is currently +in the USER-MISC package. Build LAMMPS with this package enabled using + make yes-user-misc +before compiling LAMMPS. +(See http://lammps.sandia.gov/doc/Section_start.html#start_3 for details.) + +2) This example may require additional features to be added to LAMMPS. +If LAMMPS complains about an "Invalid pair_style", then + a) download the "additional_lammps_code" from + http://moltemplate.org (upper-left corner menu) + b) unpack it + c) copy the .cpp and .h files to the src folding of your lammps installation. + d) (re)compile LAMMPS. + + +----- Details -------- + +This example contains a coarse-grained model of a 4-helix bundle protein +inserted into a lipid bilayer (made from a mixture of DPPC and DLPC). + + -- Protein Model: -- + +The coarse-grained protein is described in: + G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) +Here we use the "AUF2" model described in that paper. +(The hydrophobic beads face outwards.) + + -- Memebrane Model: -- + +The DPPC lipid bilayer described in: + G. Brannigan, P.F. Philips, and F.L.H. Brown, + Physical Review E, Vol 72, 011915 (2005) +and: + M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown + J. Chem. Phys. 135, 244701 (2011) + +As in Watson(JCP 2011), rigid bond-length constraints +have been replaced by harmonic bonds. + +A truncated version of this lipid (named "DLPC") has also been added. +The bending stiffness of each lipid has been increased to compensate +for the additional disorder resulting from mixing two different types +of lipids together. (Otherwise pores appear.) +Unlike the original "DPPC" molecule model, the new "DPPC" and "DLPC" models +have not been carefully parameterized to reproduce the correct behavior in +a lipid bilayer mixture. + + +------------- + +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_run.sh new file mode 100755 index 000000000..9598e3b08 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_run.sh @@ -0,0 +1,33 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data, and table_int.dat +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # Run a simulation at constant pressure (tension) + +#or + +lmp_linux -i run.in.nvt # Run a simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation are ignored when beginning the simulation at constant volume. +# This can be fixed. Read "run.in.nvt" for equilibration instructions.) + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#or +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_setup.sh new file mode 100755 index 000000000..abf2fce64 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_setup.sh @@ -0,0 +1,28 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # The "table_int.dat" file contains tabular data for the lipid INT-INT atom + # 1/r^2 interaction. We need it too. (This slows down the simulation by x2, + # so I might look for a way to get rid of it later.) + cp -f table_int.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_visualize.txt new file mode 100644 index 000000000..019afc144 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg new file mode 100644 index 000000000..246ee5462 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_LR.jpg new file mode 100644 index 000000000..fdbb446ee Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_no_pbc_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_no_pbc_LR.jpg new file mode 100644 index 000000000..142f3f706 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_no_pbc_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg new file mode 100644 index 000000000..5d4b15b29 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg new file mode 100644 index 000000000..285389039 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010.lt new file mode 100644 index 000000000..a5df81056 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010.lt @@ -0,0 +1,254 @@ +# This file defines a 4-helix bundle coarse-grained protein model (AUF2) used in +# G. Bellesia, AI Jewett, and J-E Shea, +# Protein Science, Vol19 141-154 (2010) +# +# Strategy: +# +#1) First I'll define some building blocks (A16, B16, T3) +# which are helices, sheets and turns of a predetermined length) +# +#2) Then I'll copy and paste them together to build +# a 4-helix bundle (or a 4-strand beta-barrel). +# This approach is optional. If your protein has helices which are not +# identical, you should probably just include all 4 helices in a single +# "Data Atoms" section and don't try to subdivide the protein into pieces.) + + + +1beadProtSci2010 { # <-- enclose definitions in a namespace for portability + + # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) + + A16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../sL 0.0 -2.4 -2.4 0.0 + $atom:a2 $mol:... @atom:../sL 0.0 2.4 -2.4 3.6 + $atom:a3 $mol:... @atom:../sH 0.0 2.4 2.4 7.2 + $atom:a4 $mol:... @atom:../sH 0.0 -2.4 2.4 10.8 + $atom:a5 $mol:... @atom:../sL 0.0 -2.4 -2.4 14.4 + $atom:a6 $mol:... @atom:../sL 0.0 2.4 -2.4 18.0 + $atom:a7 $mol:... @atom:../sH 0.0 2.4 2.4 21.6 + $atom:a8 $mol:... @atom:../sH 0.0 -2.4 2.4 25.2 + $atom:a9 $mol:... @atom:../sL 0.0 -2.4 -2.4 28.8 + $atom:a10 $mol:... @atom:../sL 0.0 2.4 -2.4 32.4 + $atom:a11 $mol:... @atom:../sH 0.0 2.4 2.4 36.0 + $atom:a12 $mol:... @atom:../sH 0.0 -2.4 2.4 39.6 + $atom:a13 $mol:... @atom:../sL 0.0 -2.4 -2.4 43.2 + $atom:a14 $mol:... @atom:../sL 0.0 2.4 -2.4 46.8 + $atom:a15 $mol:... @atom:../sH 0.0 2.4 2.4 50.4 + $atom:a16 $mol:... @atom:../sH 0.0 -2.4 2.4 54.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # A16 + + + T3 { # T3 is a "turn" region consisting of 3 beads + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../tN 0.0 -4.8 0.0 0.0 + $atom:a2 $mol:... @atom:../tN 0.0 0.0 3.3 -1.44 + $atom:a3 $mol:... @atom:../tN 0.0 4.8 0.0 0.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + } + + } # T3 + + + # ----- Now build a larger molecule using A16 and T3 ------- + + # Create a 4-Helix bundle. + # In this version, the hydrophobic beads are poing outward. + # I oriented them this way because I want to place this protein in a membrane. + # (There is another file in this directory containing alternate version + # of this same molecule with the hydrophobic beads pointing inward.) + + 4HelixInsideOut { + helix1 = new A16.rot(-225, 0,0,1).move(-5.70,-5.70,-32.4) + helix2 = new A16.rot(-135, 0,0,1).move( 5.70,-5.70,-28.8) + helix3 = new A16.rot( -45, 0,0,1).move( 5.70, 5.70,-25.2) + helix4 = new A16.rot( 45, 0,0,1).move(-5.70, 5.70,-21.6) + + turn1 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot( 10,0,0,1).move(0.78,-4.2, 27.9) + turn2 = new T3.rot(-10,1,0,0).rot( 20,0,1,0).rot(-70,0,0,1).move(4.55, 2.4,-33.0) + turn3 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot(190,0,0,1).move(-0.78,4.2, 34.2) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixInsideOut + + + # -------- Minor coordinates adjustment: ----------- + + # Those coordinates in the commands above are a little too large. + # To make it easier to type them in, I was using sigma=6.0 Angstroms. + # Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667) + + 4HelixInsideOut.scale(0.9166666666666666) + + # Note: "scale()" only effects the initial coordinates of + # the molecule, not the force field parameters. + # (If you plan to minimize the molecule, you don't need to + # be so careful about the initial coordinates. In that case, + # you don't have worry about "scale()". Feel free to remove.) + + + + # -------------- Force-Field Parameters ------------ + + # Units and force-field styles for this protein model + # (These can be overridden later.) + + write_once("In Init") { + units real + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid fourier + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 21.0 24.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + + # --- Distance Units --- + # In this version of the model, sigma (the bond-length + # and particle diameter) is rounded to 5.5 Angstroms. + # + # --- Energy & Temperature Units --- + # In this protein model, "epsilon" represents the free energy + # bonus for bringing two hydrophobic amino acids together. + # Here I choose to set epsilon to 1.806551818181818 kCal/mole. + # This value was chosen so that a temperature of 300 Kelvin lies at + # 0.33 epsilon, which is the unfolding temperature of the marginally stable + # "ASF1" protein model from the Bellesia et al 2010 paper. + # This choice insures that both the "ASF1" model from that paper, + # as well as the much more stable "AUF2" protein we use here (which + # unfolds at 0.42*eps) should definitely remain stable at 300 degrees Kelvin, + # in the bulk at least. (However it's not clear that these energy + # parameters will work well for a protein in membrane. Perhaps I'll + # run some tests and fine tune these parameters for this scenario.) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:sH @atom:sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + pair_coeff @atom:sL @atom:sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 + pair_coeff @atom:tN @atom:tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 + } + + # The exact value of the bond_coeff does not matter too much as long as + # it is "stiff enough". Here I use a softer bond spring than the one + # used in the paper so that I can increase the time step. + # I also use a relatively soft spring to constrain the bond angles. + + # bond_coeff bondType bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:1beadProtSci2010/backbone harmonic 10.0 5.5 + } + + + + # We use the same bond-angle forces whenever + # there are 3 consecutively-bonded atoms: + # + # angleType atomtypes1 2 3 bondtypes1 2 + + write_once("Data Angles By Type") { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # angle_coeff angleType anglestylename k theta0 + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 100.0 105.0 + } + + + + + # Dihedral interactions are also determined by atom-type name in this case. + # I chose atoms whose type-names begin with "t" to be "turn" atoms. + # Atoms whose type-names begin with "s" could be either helices or sheets. + # (In this case, helices. In this example, we use the @dihedral:delta65_0 + # parameters. This corresponds to the "AUF2" model from the + # Bellesia et. al 2010 paper.) + + # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 + + write_once("Data Dihedrals By Type") { + @dihedral:delta65_0 @atom:s* @atom:s* @atom:s* @atom:s* * * * + + # If "tN" (turn) atoms are present, use the @dihedral:turn parameters + + @dihedral:turn @atom:tN @atom:* @atom:* @atom:* * * * + } + + + # From the Bellesia et al 2010 paper: + # for helices: U_{dih}(\phi) = 1.2*(cos(3\phi) + cos(\phi+\delta)) + # for turns: U_{dih}(\phi) = 0.2*cos(3\phi) + # + # General formula used for "dihedral_style fourier": + # U_{dih}(\phi) = \Sum_{i=1}^m K_i [ 1.0 + cos(n_i \phi - d_i) ] + # + # Syntax: + # dihedralType dihedralstyle m K_1 n_1 d_1 K2 n_2 d_2 ... + + write_once("In Settings") { + dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0 + dihedral_coeff @dihedral:delta62_5 fourier 2 2.167862 3 0 2.167862 1 -62.5 + dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0 + dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0 + # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon. + } + + + # --- Mass Units --- + # Typical amino acids weigh approximately 110.0 grams/mole. (Rounding down): + write_once("Data Masses") { + @atom:1beadProtSci2010/sH 100.0 + @atom:1beadProtSci2010/sL 100.0 + @atom:1beadProtSci2010/tN 100.0 + } + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt new file mode 100644 index 000000000..e6e6bced7 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt @@ -0,0 +1,225 @@ +### THIS FILE IS OPTIONAL AND IS NOT NECESSARY. IN THIS FILE, I DEFINED SOME ## +### ADDITIONAL PROTEIN TYPES FROM THE PAPER THAT I DID NOT USE IN THIS EXAMPLE## +# +# This file defines a family of coarse-grained protein models used in: +# G. Bellesia, AI Jewett, and J-E Shea, +# Protein Science, Vol19 141-154 (2010) +# +# Strategy: +# +#1) First I'll define some building blocks (A16, B16, T3) +# which are helices, sheets and turns of a predetermined length) + +import "1beadProtSci2010.lt" + +# We defined A16 and T3 earlier in "1beadPRotSci2010.lt" Will define B16 below +# +#2) Then I'll copy and paste them together to build +# a 4-helix bundle or a 4-strand beta-barrel. + + +1beadProtSci2010 { #<-- Add new molecules to existing namespace defined earlier + # This way we don't have to start from scratch. We can + # use all the atom types and angle settings defined earlier + + # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) + + B16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../sL 0.0 -1.8 0.0 0.0 + $atom:a2 $mol:... @atom:../sH 0.0 1.8 0.0 4.8 + $atom:a3 $mol:... @atom:../sL 0.0 -1.8 0.0 9.6 + $atom:a4 $mol:... @atom:../sH 0.0 1.8 0.0 14.4 + $atom:a5 $mol:... @atom:../sL 0.0 -1.8 0.0 19.2 + $atom:a6 $mol:... @atom:../sH 0.0 1.8 0.0 24.0 + $atom:a7 $mol:... @atom:../sL 0.0 -1.8 0.0 28.8 + $atom:a8 $mol:... @atom:../sH 0.0 1.8 0.0 33.6 + $atom:a9 $mol:... @atom:../sL 0.0 -1.8 0.0 38.4 + $atom:a10 $mol:... @atom:../sH 0.0 1.8 0.0 43.2 + $atom:a11 $mol:... @atom:../sL 0.0 -1.8 0.0 48.0 + $atom:a12 $mol:... @atom:../sH 0.0 1.8 0.0 52.8 + $atom:a13 $mol:... @atom:../sL 0.0 -1.8 0.0 57.6 + $atom:a14 $mol:... @atom:../sH 0.0 1.8 0.0 62.4 + $atom:a15 $mol:... @atom:../sL 0.0 -1.8 0.0 67.2 + $atom:a16 $mol:... @atom:../sH 0.0 1.8 0.0 72.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # B16 + + # ----- Now build larger molecules using B16 and T3 ------- + + + 4SheetBarrel { + sheet1 = new B16.rot( 45, 0,0,1).move(-4.762203156,-4.762203156, -36.0) + sheet2 = new B16.rot( 135, 0,0,1).move( 4.762203156,-4.762203156, -36.0) + sheet3 = new B16.rot( 225, 0,0,1).move( 4.762203156, 4.762203156, -36.0) + sheet4 = new B16.rot( 315, 0,0,1).move(-4.762203156, 4.762203156, -36.0) + + turn1 = new T3.rot(180,1,0,0).rot( 0, 0,0,1).move( 0, -7.8, 39.6) + turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(4.2, 0.0,-41.4) + turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move( 0, 7.8, 39.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + # Below I define several alternate conformations of the"4HelixBundleInsideOut" + # molecule I defined earlier in "1beadProtSci2010.lt". Same molecule however. + + 4HelixBundle { + helix1 = new A16.rot( -45, 0,0,1).move(-5.70,-5.70,-32.4) + helix2 = new A16.rot( 45, 0,0,1).move( 5.70,-5.70,-28.8) + helix3 = new A16.rot( 135, 0,0,1).move( 5.70, 5.70,-25.2) + helix4 = new A16.rot( 225, 0,0,1).move(-5.70, 5.70,-21.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + + turn1 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot( 8,0,0,1).move(-3.6,-4.8,28.2) + turn2 = new T3.rot(-5,1,0,0).rot( 21,0,1,0).rot(-100,0,0,1).move(4.2,-0.66,-30.9) + turn3 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot(188,0,0,1).move(3.6,4.8,35.4) + + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixBundle + + + + + # --- alternate conformations (same molecule) ---- + + # In the following version, the helices are oriented in a similar way, + # but they are separated a little further away from eachother. + + 4HelixBundleLoose { + + helix1 = new A16.rot( -45, 0,0,1).move(-6.7347723,-6.7347723, -27.0) + helix2 = new A16.rot( 45, 0,0,1).move( 6.7347723,-6.7347723, -27.0) + helix3 = new A16.rot( 135, 0,0,1).move( 6.7347723, 6.7347723, -27.0) + helix4 = new A16.rot( 225, 0,0,1).move(-6.7347723, 6.7347723, -27.0) + + turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-1.2,-4.2,32.4) + turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(4.2,-0.9,-28.8) + turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(1.2,4.2,32.4) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + # In following version, the helices are oriented in a similar way, + # but they are separated a little further away from eachother. + + 4HelixInsideOutLoose { + helix1 = new A16.rot(-225, 0,0,1).move(-6.7347723,-6.7347723, -27.0) + helix2 = new A16.rot(-135, 0,0,1).move( 6.7347723,-6.7347723, -27.0) + helix3 = new A16.rot( -45, 0,0,1).move( 6.7347723, 6.7347723, -27.0) + helix4 = new A16.rot( 45, 0,0,1).move(-6.7347723, 6.7347723, -27.0) + + turn1 = new T3.rot(180,1,0,0).rot( 10,0,0,1).move( 0.78,-4.2,28.8) + turn2 = new T3.rot( 70,1,0,0).rot(-70,0,0,1).move( 10.8,2.4,-28.2) + turn3 = new T3.rot(180,1,0,0).rot(190,0,0,1).move(-0.78,4.2,28.8) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixInsideOutLoose + + + + + # In the following version, the 4 helices are arranged next to each other, + # side-by-side, in a planar conformation (instead of a compact bundle). + + 4HelixPlanar { + helix1 = new A16.rot(-00, 0,0,1).move(0, 0, -27.0) + helix2 = new A16.rot( 00, 0,0,1).move(14.4, 0, -27.0) + helix3 = new A16.rot(-00, 0,0,1).move(28.8, 0, -27.0) + helix4 = new A16.rot( 00, 0,0,1).move(43.2, 0, -27.0) + + turn1 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move( 4.8, 0, 31.8) + turn2 = new T3.rot( 0,1,0,0).rot(180,0,0,1).move(19.2, 0,-31.8) + turn3 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move(34.6, 0, 31.8) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixPlanar + + + # -------- Minor coordinates adjustment: ----------- + # Those coordinates in the commands above are a little too large. + # To make it easier to type them in, I was using sigma=6.0 Angstroms. + # Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667) + + 4SheetBarrel.scale(0.9166666666666666) + 4HelixBundle.scale(0.9166666666666666) + 4HelixBundleLoose.scale(0.9166666666666666) + 4HelixInsideOutLoose.scale(0.9166666666666666) + 4HelixPlanar.scale(0.9166666666666666) + + # Note: "scale()" only effects the initial coordinates of + # the molecule, not the force field parameters. + # (If you plan to minimize the molecule, you don't need to + # be so careful about the initial coordinates. In that case, + # you don't have worry about "scale()". Feel free to remove.) + + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/CGLipidBr2005.lt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/CGLipidBr2005.lt new file mode 100644 index 000000000..3b39048f7 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/CGLipidBr2005.lt @@ -0,0 +1,198 @@ +# Note: +# +# This example may require additional features to be added to LAMMPS. If +# LAMMPS complains about an "Invalid pair_style", then download copy the +# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS +# "src" directory and recompile LAMMPS. +# +# -------- Description -------- +# +# This example contains an implementation of the DPPC lipid bilayer described in +# G. Brannigan, P.F. Philips, and F.L.H. Brown, +# Physical Review E, Vol 72, 011915 (2005) +# and: +# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown +# J. Chem. Phys. 135, 244701 (2011) +# +# As in Watson(JCP 2011), rigid bond-length constraints have been replaced +# by harmonic bonds. +# +# A truncated version of this lipid (named "DLPC") has also been added. +# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully +# parameterized to reproduce the correct behavior in a lipid bilayer mixture. +# +# Units: +# +# The "epsilon" parameter in their model is approximately 2.75 kJ/mole +# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ) +# The "sigma" parameter corresponds to 7.5 angstroms. + + +CGLipidBr2005 { + + + write_once("In Init") { + # -- Default styles for "CGLipidBr2005" -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + + #angle_style hybrid cosine/delta # <- used in the original article + angle_style hybrid harmonic # <- prevents unphysical acute angle turns + # Explanation: + # angle_style cosine/delta: U(theta) = k*(1-cos(theta-theta0)) + # angle_style harmonic: U(theta) = k*(theta-theta0)^2 + + dihedral_style none + improper_style none + pair_style hybrid table linear 1130 & + lj/charmm/coul/charmm/inter es4k4l 14.5 15 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" + + neighbor 2.0 multi # <- perhaps unnecessary + communicate multi # <- perhaps unnecessary + } + + + DPPC { + write("Data Atoms") { + $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom + $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25 + $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75 + $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25 + $atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75 + } + write("Data Bonds") { + $bond:b1 @bond:../backbone $atom:h $atom:i + $bond:b2 @bond:../backbone $atom:i $atom:t1 + $bond:b3 @bond:../backbone $atom:t1 $atom:t2 + $bond:b4 @bond:../backbone $atom:t2 $atom:t3 + } + write("Data Angles") { + $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 + $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 + $angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3 + } + + # Define properties of the local (lipid-specific) atom:head type atom: + write_once("Data Masses") { + @atom:head 200.0 + } + write_once("In Settings") { + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + } + + } #DPPC + + + DLPC { + write("Data Atoms") { + $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom + $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50 + $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00 + $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50 + } + write("Data Bonds") { + $bond:b1 @bond:../backbone $atom:h $atom:i + $bond:b2 @bond:../backbone $atom:i $atom:t1 + $bond:b3 @bond:../backbone $atom:t1 $atom:t2 + } + write("Data Angles") { + $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 + $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 + } + # Define properties of the local (lipid-specific) atom:head type atom: + write_once("Data Masses") { + @atom:head 200.0 + } + write_once("In Settings") { + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + } + } #DLPC + + + # Particles and properties shared by all lipid types: + + write_once("Data Masses") { + @atom:int 200.0 + @atom:tail 200.0 + @atom:head 200.0 #<- Default head type. We may override it later. + } + + write_once("In Settings") { + # -- Default settings/parameters for "CGLipidBr2005" -- + # (Hybrid bond & angle styles were used for portability.) + + # As in Watson(JCP 2011), rigid bond-length constraints + # have been replaced by harmonic bonds. + # The k_theta parameter should lie in between 5*epsilon and 10*epsilon. + bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2 + } + + write_once("In Settings") { + # cosine/delta: U(theta) = k*(1-cos(theta-theta0)) + #angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps + # harmonic: U(theta) = k*(theta-theta0)^2 not (k/2)*(theta-theta0)^2 + angle_coeff @angle:backbone harmonic 9.85898661 180 #<-->30*eps + } + # I use a stiffer bond-angle than the original Brannigan & Brown 2005 paper + # to attempt to compensate for the fact that here we are using a lipid + # mixture of DPPC and DLPC. (The mixture of lipids introduces a great deal + # of disorder into the bilayer which would not be present in a DPPC bilayer. + # This causes pores to form. Increasing the angle stiffness prevents this.) + + write_once("In Settings") { + + # The interaction of "atom:int" with other "atom:int" atoms is given by + # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at + # r=3*sigma. This was implemented using pair_style table. + # Unfortunately, mixing lj/charmm and "table" pair styles in the same + # simulation is very inneficient. + + pair_coeff @atom:int @atom:int table table_int.dat INT + + # The interaction of tail beads with eachother is given by the formula below + # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules: + # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6), + pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + + # The interaction of head beads which all other beads is given by: + # epsilon*(0.4*(sigma/r)^12 - 0.0*(sigma/r)^6), + + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + + } # write_once("In Settings") + + # Note: I divided epsilon by 4 to get "0.1643" because we are using the + # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6) + # (The "es4k4l" coeffstyle is the default.) Using this convention makes it + # easier to mix this coarse-grained lipid model with other molecular models. + + + +} # CGLipidBr2005 + + + + + + + + +# Note: This example has not been optimized for speed. +# +# Unfortunately, using both lj/charmm and "table" pair styles in the same +# simulation seems to be very inneficient. (The simulation is twice as slow +# as using only the "lj/charmm" pair styles for every pairwise interaction, +# ...and about 25% slower than using "table" for every pairwise interaction. +# However the lennard-jones pair styles support mixing, so we use them to +# make it easier to run these molecules with other molecules which don't use +# pair_table. I felt that portability was worth the extra 25% slow down.) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py new file mode 100755 index 000000000..0d09e4d02 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py @@ -0,0 +1,29 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between "INT" atoms +# in the lipid membrane model described in +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) +# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity) + +def U(r, eps, sigma): + return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) +def F(r, eps, sigma): + return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) + +epsilon = 2.75/4.184 # kCal/mole +sigma = 7.5 +Rmin = 0.02 +Rmax = 22.6 +rcut = 22.5 +N = 1130 + +for i in range(0,N): + r = Rmin + i*(Rmax-Rmin)/(N-1) + U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma) + F_r = F(r, epsilon, sigma) + if r > rcut: + U_r = 0.0 + F_r = 0.0 + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py new file mode 100755 index 000000000..32147e444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py @@ -0,0 +1,70 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between "INT" atoms +# in the lipid membrane model described in +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) +# I realized later this is not what we want because although energy is conserved +# all enrgies are shifted with respect to energies used in the Brannigan paper +# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole). +# (So don't use this.) + +# Calculate and print a + +def S(r, rc1, rc2, derivative=False): + """ + Calculate the switching function S(r) which decays continuously + between 1 and 0 in the range from rc1 to rc2 (rc2>rc1): + S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3 + I'm using the same smoothing/switching cutoff function used by the CHARMM + force-fields. (I'm even using the same code to implement it, taken + from lammps charmm/coul/charmm pair style, rewritten in python.) + + """ + assert(rc2>rc1) + rsq = r*r + rc1sq = rc1*rc1 + rc2sq = rc2*rc2 + denom_lj_inv = (1.0 / ((rc2sq-rc1sq)* + (rc2sq-rc1sq)* + (rc2sq-rc1sq))) + if rsq > rc2sq: + return 0.0 + elif rsq < rc1sq: + if derivative: + return 0.0 + else: + return 1.0 + else: + rc2sq_minus_rsq = (rc2sq - rsq) + rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq + if derivative: + return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv) + else: + return (rc2sq_minus_rsq_sq * + (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv) + + +def U(r, eps, sigma): + return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) + +def F(r, eps, sigma): + return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) + +epsilon = 2.75/4.184 # kCal/mole +sigma = 7.5 +Rmin = 0.02 +Rmax = 22.6 +Rc1 = 22.0 +Rc2 = 22.5 +N = 1130 + +for i in range(0,N): + r = Rmin + i*(Rmax-Rmin)/(N-1) + U_r = U(r, epsilon, sigma) + F_r = F(r, epsilon, sigma) + # Multiply U(r) & F(r) by the smoothing/switch function + U_r = U_r * S(r, Rc1, Rc2) + F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False) + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/system.lt new file mode 100644 index 000000000..51a67b6d9 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/system.lt @@ -0,0 +1,207 @@ +# Description: + +# This example shows how to put a protein (inclusion) in a +# lipid bilayer mixture composed of two different lipids (DPPC and DLPC). +# The DPPC lipid model is described here: +# G. Brannigan, P.F. Philips, and F.L.H. Brown, +# Physical Review E, Vol 72, 011915 (2005) +# The protein model is described here: +# G. Bellesia, AI Jewett, and J-E Shea, +# Protein Science, Vol19 141-154 (2010) +# The new DLPC model is a truncated version of DPPC, +# (Its behaviour has not been rigorously tested.) +# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to +# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293 + +# Note: +# This example may require additional features to be added to LAMMPS. +# If LAMMPS complains about an "Invalid pair_style", then copy the code +# in the "additional_lammps_code" directory into your LAMMPS "src" directory +# and recompile LAMMPS. + + + +import "CGLipidBr2005.lt" + +using namespace CGLipidBr2005 + +# The "= new random" syntax chooses one of several molecules at random + +lipids = new random([DPPC, DLPC], [0.5,0.5], 1234) #"1234"=random_seed + [13].move(7.5, 0, 0) + [15].move(3.75, 6.49519, 0) # <-- hexagonal lattice + [2].rot(180, 1, 0, 0) # <-- 2 monolayers + +# Move all the lipds up to the center of the box + +lipids[*][*][*].move(0,0,75.0) + + + + +# Although this patch of lipids is not square or rectangular, (it looks +# like a parallelogram), this is no longer the case after rectangular +# periodic boundary conditions are applied. (Check by visualising in VMD.) + + +write_once("Data Boundary") { + 0 97.5 xlo xhi + 0 97.42785792 ylo yhi + 0 150.0 zlo zhi +} + + +# A note on geometry: +# We want to create a bilayer arranged in a hexagonal lattice consisting of +# 15 rows (each row is aligned with the x-axis) +# 13 columns (aligned at a 60 degree angle from the x axis) +# The lattice spacing is 7.5 Angstroms. +# When wrapped onto a rectangular box, the dimensions of the system are: +# 13 * 7.5 Angstroms in the X direction +# 15 * 7.5*sqrt(3)/2 Angstroms in the Y direction + + + + + + + +# ------------------- protein inclusion --------------------- + +import "1beadProtSci2010.lt" + +using namespace 1beadProtSci2010 + +protein = new 4HelixInsideOut + +protein.move(45.0, 25.98076211, 75.0) + + +# Delete a hole in the membrane to create space for the protein. + +delete lipids[4][2][*] +delete lipids[6][2][*] +delete lipids[3-6][3][*] +delete lipids[3-5][4][*] +delete lipids[2-5][5][*] +delete lipids[2][6][*] +delete lipids[4][6][*] + +# Note: All atom types must include the full path (the name of +# the namespace which defined them as well as the atom type name). +# (This is because we are no longer inside that namespace.) + + +write_once("In Settings") { + + # ----------------------------------------------------------- + # -------- interactions between protein and lipids ---------- + # ----------------------------------------------------------- + + # Interactions between the protein and lipid atoms are usually + # determined by mixing rules. (However this is not possible some + # for atoms, such as the "int" atoms in the lipid model which + # interact using -1/r^2 attraction.) Mixing rules do not make + # sense for these atoms so we must explicitly define their + # interaction with all other atoms. + + # We want the hydrophobic interactions between hydrophobic residues in + # the protein and beads the interior of the lipid to be energetically + # similar to the attractive interactions between the lipid tails. + # + # Note: I made the width of the outward-facing protein beads slightly larger + # ("12.5") whenever they interact with the "tail" beads in each lipid + # (in order to make the protein wider there). + # This hopefully relieves some of the internal negative pressure in the center + # of the bilayer which can otherwise rip apart the protein or suck it into + # the bilaer. (This is a hack, and I'm not sure if it is necessary. + # For different protein or lipid models, you probably don't need this.) + # + # i j pairstylename eps sig K L + + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 12.5 0.4 -1 + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + + # To help keep the protein from tilting 90 degrees and burying itself + # within the lipid bilayer, we make the turn regions at either + # end of the protein (strongly) attracted to the head groups + # of the lipid. (In reality, they would probably be attracted + # to the water as well.) + + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + + # All other interactions between proteins and lipids are steric. + + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + + # ----------------------------------------------------------- + # -------- Modifications to the protein model: -------------- + # ----------------------------------------------------------- + # + # Turn off attraction between the hydrophobic "@atom:sH" beads: + # (These beads are located in the outside of a trans-membrane protein.) + + pair_coeff @atom:1beadProtSci2010/sH @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 + + # (Why: These beads are only attracted to + # each other in an aqueous environment) + + # ... and + # Turn ON attraction between the hydrophilic "@atom:sL" beads. + # (These beads are located in the interior of a trans-membrane protein.) + + pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + + # Why? + # In reality, polar groups in the interior of trans-membrane + # proteins do form hydrogen bonds with each other. This was + # absent from the original protein model because, in an aqueous + # environment, these groups preferentially interact with the water. + # + # Why is this necessary? + # Shouldn't attraction between lipid tails and the protein create + # an effective force which brings the hydrophilic beads together? + # (similar to the hydrophobic effect, but in reverse?). + # Answer: + # Unlike an aqueous environment (~zero pressure, or +1atm), there is + # a large negative pressure in the interior of some bilayer membrane + # models (such as this one). Without some kind of direct attraction + # between interior residues, the protein will get pulled apart. + # (Perhaps the attractive force I am using is too strong?) + +} + + + + +# Finally, we must combine the two force-field styles which were used for +# the coarse-grained lipid and protein. To do that, we write one last time +# to the "In Init" section. When reading the "Init" section LAMMPS will +# read these commands last and this will override any earlier settings. + +write_once("In Init") { + # -- These styles override earlier settings -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + angle_style hybrid cosine/delta harmonic + dihedral_style hybrid fourier + improper_style none + pair_style hybrid table linear 1130 lj/charmm/coul/charmm/inter es4k4l 14.5 15 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" +} + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/table_int.dat b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/table_int.dat new file mode 100644 index 000000000..b0d651d67 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/table_int.dat @@ -0,0 +1,1139 @@ +# Table for the INT-INT interaction from +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# This table contains +# i r_i U(r_i) -dU/dr|r_i +# where U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) + +INT +N 1130 + +1 0.02 2.0331818401e+30 1.21990910406e+33 +2 0.04 4.9638228518e+26 1.48914685554e+29 +3 0.06 3.82579033251e+24 7.65158066501e+26 +4 0.08 1.21187081343e+23 1.81780622014e+25 +5 0.1 8.32791281704e+21 9.99349538045e+23 +6 0.12 9.34030842897e+20 9.34030842897e+22 +7 0.14 1.46892540453e+20 1.25907891817e+22 +8 0.16 2.95866897809e+19 2.21900173357e+21 +9 0.18 7.19889946863e+18 4.79926631242e+20 +10 0.2 2.0331818401e+18 1.21990910406e+20 +11 0.22 6.47834392264e+17 3.53364213962e+19 +12 0.24 2.28034873754e+17 1.14017436877e+19 +13 0.26 8.72681951932e+16 4.02776285507e+18 +14 0.28 3.58624366341e+16 1.53696157003e+18 +15 0.3 1.56704372019e+16 6.26817488078e+17 +16 0.32 7.2233129348e+15 2.70874235055e+17 +17 0.34 3.48970861422e+15 1.23166186384e+17 +18 0.36 1.75754381558e+15 5.85847938527e+16 +19 0.38 9.18613895646e+14 2.90088598625e+16 +20 0.4 4.96382285179e+14 1.48914685554e+16 +21 0.42 2.76404230108e+14 7.89726371739e+15 +22 0.44 1.58162693423e+14 4.31352800247e+15 +23 0.46 9.27773983256e+13 2.42027995633e+15 +24 0.48 5.56725765996e+13 1.391814415e+15 +25 0.5 3.41111308981e+13 8.18667141564e+14 +26 0.52 2.13057117167e+13 4.91670270393e+14 +27 0.54 1.35459994024e+13 3.0102220895e+14 +28 0.56 8.75547769351e+12 1.87617379153e+14 +29 0.58 5.74645813711e+12 1.18892237325e+14 +30 0.6 3.8257903322e+12 7.65158066491e+13 +31 0.62 2.58128463312e+12 4.99603477424e+13 +32 0.64 1.7635041342e+12 3.30657025205e+13 +33 0.66 1.21901470178e+12 2.21639036726e+13 +34 0.68 8.51979641904e+11 1.50349348607e+13 +35 0.7 6.0167184547e+11 1.0314374497e+13 +36 0.72 4.29087845387e+11 7.15146409276e+12 +37 0.74 3.08855637556e+11 5.00846980094e+12 +38 0.76 2.24270970425e+11 3.54112058818e+12 +39 0.78 1.64210505205e+11 2.52631546702e+12 +40 0.8 1.2118708117e+11 1.81780621971e+12 +41 0.82 90109367359.1 1.31867367068e+12 +42 0.84 67481501334.4 9.64021449503e+11 +43 0.86 50880896383.4 7.09965997788e+11 +44 0.88 38613938681.2 5.26553710913e+11 +45 0.9 29486692086.8 3.93155896009e+11 +46 0.92 22650731882.4 2.95444330322e+11 +47 0.94 17498544395.3 2.23385674464e+11 +48 0.96 13591937526.4 1.69899220331e+11 +49 0.98 10612635712.6 1.29950642555e+11 +50 1.0 8327912706.34 99934953582.6 +51 1.02 6566502316.69 77252969474.2 +52 1.04 5201589672.36 60018343356.8 +53 1.06 4138717434.11 46853405843.3 +54 1.08 3307128665.58 36745874940.0 +55 1.1 2653529579.27 28947596241.1 +56 1.12 2137567708.15 22902511945.9 +57 1.14 1728534024.3 18195095739.0 +58 1.16 1402943799.0 14513212422.1 +59 1.18 1142752163.37 11621209113.9 +60 1.2 934030766.093 9340308300.6 +61 1.22 765981286.774 7534242773.65 +62 1.24 630196371.787 6098675145.29 +63 1.26 520103253.414 4953364870.6 +64 1.28 430542934.103 4036340534.04 +65 1.3 357450462.101 3299543229.91 +66 1.32 297610947.802 2705554551.18 +67 1.34 248472587.186 2225128105.44 +68 1.36 208002782.573 1835319108.76 +69 1.38 174576985.011 1518061159.35 +70 1.4 146892484.084 1259078837.33 +71 1.42 123901294.937 1047053582.16 +72 1.44 104757721.536 872981382.419 +73 1.46 88777241.639 729676313.267 +74 1.48 75404158.02 611385405.387 +75 1.5 64186061.7033 513488820.507 +76 1.52 54753607.1486 432265633.695 +77 1.54 46804443.7318 364710253.134 +78 1.56 40090410.0598 308388060.159 +79 1.58 34407297.9713 261321529.95 +80 1.6 29586646.6744 221900119.2 +81 1.62 25489145.661 188808745.634 +82 1.64 21999316.2868 160970856.824 +83 1.66 19021212.5921 137502982.517 +84 1.68 16474936.8715 117678352.86 +85 1.7 14293808.3245 100897694.735 +86 1.72 12422056.6082 86665727.6626 +87 1.74 10812938.3788 74572197.8496 +88 1.76 9427195.57103 64276535.39 +89 1.78 8231790.46096 55495411.7777 +90 1.8 7198865.45512 47992625.088 +91 1.82 6304885.77339 41570857.9644 +92 1.84 5529931.32911 36064946.1544 +93 1.86 4857110.59557 31336368.341 +94 1.88 4272074.43377 27268725.7382 +95 1.9 3762612.01167 23764025.6584 +96 1.92 3318314.28383 20739619.609 +97 1.94 2930293.18879 18125675.4316 +98 1.96 2590946.89128 15863086.114 +99 1.98 2293763.15199 13901736.4186 +100 2.0 2033154.33079 12199063.3122 +101 2.02 1804318.68586 10718858.1296 +102 2.04 1603123.57305 9430268.02169 +103 2.06 1426006.91783 8306962.01537 +104 2.08 1269893.96121 7326433.30293 +105 2.1 1132126.79514 6469414.48445 +106 2.12 1010404.62602 5719386.63441 +107 2.14 902733.052344 5062166.44376 +108 2.16 807380.928986 4485558.44681 +109 2.18 722843.627253 3979061.59742 +110 2.2 647811.695319 3533621.30686 +111 2.22 581144.085827 3141419.57242 +112 2.24 521845.251959 2795697.07302 +113 2.26 469045.525153 2490602.13576 +114 2.28 421984.280794 2221062.32522 +115 2.3 379995.475978 1982675.10836 +116 2.32 342495.208369 1771614.62868 +117 2.34 308970.999537 1584552.10475 +118 2.36 278972.551763 1418587.76828 +119 2.38 252103.765513 1271192.59046 +120 2.4 228015.837009 1140158.32224 +121 2.42 206401.282366 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-0.00354788564052 -0.0199492167196 +1117 22.34 -0.0031494369093 -0.0198956883597 +1118 22.36 -0.00275205683071 -0.0198423513132 +1119 22.38 -0.00235574158704 -0.0197892047262 +1120 22.4 -0.00196048737759 -0.0197362477497 +1121 22.42 -0.00156629041861 -0.0196834795391 +1122 22.44 -0.00117314694319 -0.0196308992543 +1123 22.46 -0.000781053201174 -0.0195785060596 +1124 22.48 -0.000390005459079 -0.019526299124 +1125 22.5 0.0 -0.0194742776206 +1126 22.52 0.0 0.0 +1127 22.54 0.0 0.0 +1128 22.56 0.0 0.0 +1129 22.58 0.0 0.0 +1130 22.6 0.0 0.0 diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.min b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.min new file mode 100644 index 000000000..fb2d3ddd8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.min @@ -0,0 +1,35 @@ +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# So, after typing "make yes-user-misc" in to the shell, ... +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. +# +# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" +# then you made a mistake in the instructions above. + + + +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt new file mode 100644 index 000000000..2dc4bbe03 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt @@ -0,0 +1,65 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# So, after typing "make yes-user-misc" in to the shell, ... +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. +# +# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" +# then you made a mistake in the instructions above. +# + +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + +#minimize 1.0e-5 1.0e-7 500 2000 + +timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs +dump 1 all custom 10000 traj_npt.lammpstrj id mol type x y z ix iy iz + + +thermo_style custom step temp pe etotal vol epair ebond eangle +thermo 1000 # time interval for printing out "thermo" data + + +fix fxlan all langevin 300.0 300.0 120 48279 +fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy + + +# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon +# (for the "epsilon" used by the coarse-grained lipid), and +# to 0.33*epsilon (for the "epsilon" used in the coarse-grained protein) +# Note: The langevin damping parameter "120" corresponds to +# the 0.12ps damping time used in Watson et. al JCP 2011. +# Note: We maintain the system system at constant (zero) tention +# using a barostat damping parameter Pdamp=1000 ("0 0 1000") + + +# optional (not sure if this helps): +# balance x uniform y uniform + + +run 100000 + +write_data system_after_npt.data diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt new file mode 100644 index 000000000..c9195b4e6 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt @@ -0,0 +1,71 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) +# +# -------- LAMMPS REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# So, after typing "make yes-user-misc" in to the shell, ... +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. +# +# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" +# then you made a mistake in the instructions above. +# +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs +dump 1 all custom 10000 traj_nvt.lammpstrj id mol type x y z ix iy iz + + +thermo_style custom step temp pe etotal vol epair ebond eangle +thermo 1000 # time interval for printing out "thermo" data + + +fix fxlan all langevin 300.0 300.0 120 48279 +fix fxnve all nve + +# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB. +# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon. +# Note: The langevin damping parameter "120" corresponds to +# the 0.12ps damping time used in Watson et. al JCP 2011. + +#restart 500000 + +run 10000000 + + +write_data system_after_nvt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also.) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README.TXT b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README.TXT new file mode 100644 index 000000000..1bf9d00b9 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README.TXT @@ -0,0 +1,33 @@ +Note: + This example may require additional features to be added to LAMMPS. +If LAMMPS complains about an "Invalid pair_style", then copy the code +in the "additional_lammps_code" directory into your LAMMPS "src" directory +and recompile LAMMPS. + +----- Description -------- + +This example contains an implementation of the DPPC lipid bilayer described in: + G. Brannigan, P.F. Philips, and F.L.H. Brown, + Physical Review E, Vol 72, 011915 (2005) +and: + M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown + J. Chem. Phys. 135, 244701 (2011) + +As in Watson(JCP 2011), rigid bond-length constraints +have been replaced by harmonic bonds. + +A truncated version of this lipid (named "DLPC") has also been added. +Unlike the original "DPPC" molecule model, "DLPC" has not been carefully +parameterized to reproduce the correct behavior in a lipid bilayer. + + +------------- + +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_run.sh new file mode 100755 index 000000000..9598e3b08 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_run.sh @@ -0,0 +1,33 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data, and table_int.dat +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # Run a simulation at constant pressure (tension) + +#or + +lmp_linux -i run.in.nvt # Run a simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation are ignored when beginning the simulation at constant volume. +# This can be fixed. Read "run.in.nvt" for equilibration instructions.) + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#or +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_setup.sh new file mode 100755 index 000000000..abf2fce64 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_setup.sh @@ -0,0 +1,28 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # The "table_int.dat" file contains tabular data for the lipid INT-INT atom + # 1/r^2 interaction. We need it too. (This slows down the simulation by x2, + # so I might look for a way to get rid of it later.) + cp -f table_int.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_visualize.txt new file mode 100644 index 000000000..019afc144 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DLPC.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DLPC.jpg new file mode 100644 index 000000000..637f2f1c7 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DLPC.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg new file mode 100644 index 000000000..14f1a1ed2 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg new file mode 100644 index 000000000..757abe268 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg new file mode 100644 index 000000000..2322449c1 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC.jpg new file mode 100644 index 000000000..57e093023 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt new file mode 100644 index 000000000..c0478f142 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt @@ -0,0 +1,191 @@ +# Note: +# +# This example may require additional features to be added to LAMMPS. If +# LAMMPS complains about an "Invalid pair_style", then download copy the +# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS +# "src" directory and recompile LAMMPS. +# +# -------- Description -------- +# +# This example contains an implementation of the DPPC lipid bilayer described in +# G. Brannigan, P.F. Philips, and F.L.H. Brown, +# Physical Review E, Vol 72, 011915 (2005) +# and: +# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown +# J. Chem. Phys. 135, 244701 (2011) +# +# As in Watson(JCP 2011), rigid bond-length constraints have been replaced +# by harmonic bonds. +# +# --- DLPC lipids --- +# A truncated version of the DPPC lipid (named "DLPC") has also been added. +# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully +# parameterized to reproduce the correct behavior in a lipid bilayer/mixture. +# (You may need to stiffen the bond-angle forces to make it behave correctly, +# but I did not do this here.) +# +# Units: +# +# The "epsilon" parameter in their model is approximately 2.75 kJ/mole +# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ) +# The "sigma" parameter corresponds to 7.5 angstroms. +# +# +# The new DLPC model is a truncated version of DPPC, +# (Its behaviour has not been rigorously tested.) + + +CGLipidBr2005 { + + + write_once("In Init") { + # -- Default styles for "CGLipidBr2005" -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + angle_style hybrid cosine/delta + dihedral_style none + improper_style none + pair_style hybrid table linear 1001 & + lj/charmm/coul/charmm/inter es4k4l 14.5 15 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" + + neighbor 2.0 multi # <- perhaps unnecessary + communicate multi # <- perhaps unnecessary + } + + + DPPC { + write("Data Atoms") { + $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom + $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25 + $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75 + $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25 + $atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75 + } + write("Data Bonds") { + $bond:b1 @bond:../backbone $atom:h $atom:i + $bond:b2 @bond:../backbone $atom:i $atom:t1 + $bond:b3 @bond:../backbone $atom:t1 $atom:t2 + $bond:b4 @bond:../backbone $atom:t2 $atom:t3 + } + write("Data Angles") { + $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 + $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 + $angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3 + } + + # Define properties of the local (lipid-specific) atom:head type atom: + write_once("Data Masses") { + @atom:head 200.0 + } + write_once("In Settings") { + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + } + + } #DPPC + + + DLPC { + write("Data Atoms") { + $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom + $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50 + $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00 + $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50 + } + write("Data Bonds") { + $bond:b1 @bond:../backbone $atom:h $atom:i + $bond:b2 @bond:../backbone $atom:i $atom:t1 + $bond:b3 @bond:../backbone $atom:t1 $atom:t2 + } + write("Data Angles") { + $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 + $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 + } + # Define properties of the local (lipid-specific) atom:head type atom: + write_once("Data Masses") { + @atom:head 200.0 + } + write_once("In Settings") { + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + } + } #DLPC + + + # Particles shared by all lipid types + write_once("Data Masses") { + @atom:int 200.0 + @atom:tail 200.0 + @atom:head 200.0 #<- Default head type. We may override it later. + } + + write_once("In Settings") { + # -- Default settings/parameters for "CGLipidBr2005" -- + # (Hybrid bond & angle styles were used for portability.) + + # As in Watson(JCP 2011), rigid bond-length constraints + # have been replaced by harmonic bonds. + # The k_theta parameter should lie in between 5*epsilon and 10*epsilon. + bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2 + } + + write_once("In Settings") { + angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps + #angle_coeff @angle:backbone cosine/delta 6.57265774 180 #<-- 10*eps + } + + write_once("In Settings") { + + # The interaction of "atom:int" with other "atom:int" atoms is given by + # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at + # r=3*sigma. This was implemented using pair_style table. + # Unfortunately, mixing lj/charmm and "table" pair styles in the same + # simulation is very inneficient. + + pair_coeff @atom:int @atom:int table table_int.dat INT + + # The interaction of tail beads with eachother is given by the formula below + # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules: + # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6), + pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + + # The interaction of head beads which all other beads is given by: + # epsilon*(0.4*(sigma/r)^12 - 0.0*(sigma/r)^6), + + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + + } # write_once("In Settings") + + # Note: I divided epsilon by 4 to get "0.1643" because we are using the + # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6) + # (The "es4k4l" coeffstyle is the default.) Using this convention makes it + # easier to mix this coarse-grained lipid model with other molecular models. + + + +} # CGLipidBr2005 + + + + + + + + +# Note: This example has not been optimized for speed. +# +# Unfortunately, using both lj/charmm and "table" pair styles in the same +# simulation seems to be very inneficient. (The simulation is twice as slow +# as using only the "lj/charmm" pair styles for every pairwise interaction, +# ...and about 25% slower than using "table" for every pairwise interaction. +# However the lennard-jones pair styles support mixing, so we use them to +# make it easier to run these molecules with other molecules which don't use +# pair_table. I felt that portability was worth the extra 25% slow down.) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py new file mode 100755 index 000000000..0d09e4d02 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py @@ -0,0 +1,29 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between "INT" atoms +# in the lipid membrane model described in +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) +# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity) + +def U(r, eps, sigma): + return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) +def F(r, eps, sigma): + return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) + +epsilon = 2.75/4.184 # kCal/mole +sigma = 7.5 +Rmin = 0.02 +Rmax = 22.6 +rcut = 22.5 +N = 1130 + +for i in range(0,N): + r = Rmin + i*(Rmax-Rmin)/(N-1) + U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma) + F_r = F(r, epsilon, sigma) + if r > rcut: + U_r = 0.0 + F_r = 0.0 + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py new file mode 100755 index 000000000..32147e444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py @@ -0,0 +1,70 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between "INT" atoms +# in the lipid membrane model described in +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) +# I realized later this is not what we want because although energy is conserved +# all enrgies are shifted with respect to energies used in the Brannigan paper +# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole). +# (So don't use this.) + +# Calculate and print a + +def S(r, rc1, rc2, derivative=False): + """ + Calculate the switching function S(r) which decays continuously + between 1 and 0 in the range from rc1 to rc2 (rc2>rc1): + S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3 + I'm using the same smoothing/switching cutoff function used by the CHARMM + force-fields. (I'm even using the same code to implement it, taken + from lammps charmm/coul/charmm pair style, rewritten in python.) + + """ + assert(rc2>rc1) + rsq = r*r + rc1sq = rc1*rc1 + rc2sq = rc2*rc2 + denom_lj_inv = (1.0 / ((rc2sq-rc1sq)* + (rc2sq-rc1sq)* + (rc2sq-rc1sq))) + if rsq > rc2sq: + return 0.0 + elif rsq < rc1sq: + if derivative: + return 0.0 + else: + return 1.0 + else: + rc2sq_minus_rsq = (rc2sq - rsq) + rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq + if derivative: + return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv) + else: + return (rc2sq_minus_rsq_sq * + (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv) + + +def U(r, eps, sigma): + return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) + +def F(r, eps, sigma): + return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) + +epsilon = 2.75/4.184 # kCal/mole +sigma = 7.5 +Rmin = 0.02 +Rmax = 22.6 +Rc1 = 22.0 +Rc2 = 22.5 +N = 1130 + +for i in range(0,N): + r = Rmin + i*(Rmax-Rmin)/(N-1) + U_r = U(r, epsilon, sigma) + F_r = F(r, epsilon, sigma) + # Multiply U(r) & F(r) by the smoothing/switch function + U_r = U_r * S(r, Rc1, Rc2) + F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False) + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/system.lt new file mode 100644 index 000000000..c556233c0 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/system.lt @@ -0,0 +1,94 @@ +# Description: + +# This constructs a bilayer constructed from coarse-grained DPPC lipids +# (implicit solvent). The DPPC lipid model is described here: +# G. Brannigan, P.F. Philips, and F.L.H. Brown, +# Physical Review E, Vol 72, 011915 (2005) +# +# NOTE: There is an example of a 50%/50% DPPC & DLPC mixture +# in the "membrane+protein" and "vesicle" examples. + + + + + + +import "CGLipidBr2005Orig.lt" + +using namespace CGLipidBr2005 + +lipids = new DPPC [32].move(7.5, 0, 0) + [37].move(3.75, 6.49519, 0) + [2].rot(180, 1, 0, 0) + + +# Move the lipds up to the center of the box +lipids[*][*][*].move(0,0,75.0) + + +# Although this patch of lipids is not square or rectangular, (it looks +# like a parallelogram), this is no longer the case after rectangular +# periodic boundary conditions are applied. We apply them below: +# width: 240 = 32*7.5 +# height: 240.322 = 37*6.49519 + +write_once("Data Boundary") { + 0 240 xlo xhi + 0 240.322 ylo yhi + 0 150.0 zlo zhi +} + + + + + + + + +# -------------- File ends here. Only comments below.------------------- + +# ------------------------------------ +# ------------- COMMENTS: ------------ +# ------------------------------------ +# +# A note on geometry: +# We want to create a bilayer arranged in a hexagonal lattice consisting of +# 32 rows (each row is aligned with the x-axis) +# 37 columns (aligned at a 60 degree angle from the x axis) +# The lattice spacing is 8.0 Angstroms ( ~= 0.95*sigma*2^(1/6), where sigma=7.5) +# When wrapped onto a rectangular box, the dimensions of the system are: +# 32 * 7.5 Angstroms in the X direction +# 37 * 7.5*sqrt(3)/2 Angstroms in the Y direction +# ------------------------------------ +# +# Below I show simple ways to create a lipid bilayer: +# +# 1) If you just want to make lipid bilayer out of DPPC, +# without specifying the location of each lipid, you could use this syntax: +# lipids = new DPPC [32][37][2] # 3-D array +# Later you can load in the coordinates of the lipds from a PDB file. +# Alternately you could also use a 1-dimensional array: +# lipids = new DPPC [2368] # 1-D array. Note: 2368 = 32 x 37 x 2 +# It does not matter as long as the number of lipids is correct. +# Multidimensional arrays are only useful if you plan to apply independent +# coordinate transformations to each row and column and monolayer. See below: +# +# 2) Instead of loading a PDB file later, we can directly specify the location +# of each DPPC lipid in the LT file itself. For lipid bilayers, this is +# easy, because the bilayer structure resembles 2 planar lattices. +# We can use "move" commands to place each lipid, and the "rot" command +# to turn the lipids in one of the monolayers upside down. +# +# lipids = new DPPC [32].move(7.5, 0, 0) +# [37].move(3.75, 6.49519, 0) +# [2].rot(180, 1, 0, 0) +# +# 3) If you want to create a bilayer from a mixture of DPPC and DLPC, you must +# replace "DPPC" in the command above with random([DPPC,DLPC],[0.5,0.5],12345) +# Here "0.5,0.5" are the probabilities for each molecule type, and "12345" +# is an optional random seed. +# lipids = new random([DPPC,DLPC], [0.5,0.5], 12345) +# [32].move(7.5, 0, 0) +# [37].move(3.75, 6.49519, 0) +# [2].rot(180, 1, 0, 0) +# diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/table_int.dat b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/table_int.dat new file mode 100644 index 000000000..b0d651d67 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/table_int.dat @@ -0,0 +1,1139 @@ +# Table for the INT-INT interaction from +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# This table contains +# i r_i U(r_i) -dU/dr|r_i +# where U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) + +INT +N 1130 + +1 0.02 2.0331818401e+30 1.21990910406e+33 +2 0.04 4.9638228518e+26 1.48914685554e+29 +3 0.06 3.82579033251e+24 7.65158066501e+26 +4 0.08 1.21187081343e+23 1.81780622014e+25 +5 0.1 8.32791281704e+21 9.99349538045e+23 +6 0.12 9.34030842897e+20 9.34030842897e+22 +7 0.14 1.46892540453e+20 1.25907891817e+22 +8 0.16 2.95866897809e+19 2.21900173357e+21 +9 0.18 7.19889946863e+18 4.79926631242e+20 +10 0.2 2.0331818401e+18 1.21990910406e+20 +11 0.22 6.47834392264e+17 3.53364213962e+19 +12 0.24 2.28034873754e+17 1.14017436877e+19 +13 0.26 8.72681951932e+16 4.02776285507e+18 +14 0.28 3.58624366341e+16 1.53696157003e+18 +15 0.3 1.56704372019e+16 6.26817488078e+17 +16 0.32 7.2233129348e+15 2.70874235055e+17 +17 0.34 3.48970861422e+15 1.23166186384e+17 +18 0.36 1.75754381558e+15 5.85847938527e+16 +19 0.38 9.18613895646e+14 2.90088598625e+16 +20 0.4 4.96382285179e+14 1.48914685554e+16 +21 0.42 2.76404230108e+14 7.89726371739e+15 +22 0.44 1.58162693423e+14 4.31352800247e+15 +23 0.46 9.27773983256e+13 2.42027995633e+15 +24 0.48 5.56725765996e+13 1.391814415e+15 +25 0.5 3.41111308981e+13 8.18667141564e+14 +26 0.52 2.13057117167e+13 4.91670270393e+14 +27 0.54 1.35459994024e+13 3.0102220895e+14 +28 0.56 8.75547769351e+12 1.87617379153e+14 +29 0.58 5.74645813711e+12 1.18892237325e+14 +30 0.6 3.8257903322e+12 7.65158066491e+13 +31 0.62 2.58128463312e+12 4.99603477424e+13 +32 0.64 1.7635041342e+12 3.30657025205e+13 +33 0.66 1.21901470178e+12 2.21639036726e+13 +34 0.68 8.51979641904e+11 1.50349348607e+13 +35 0.7 6.0167184547e+11 1.0314374497e+13 +36 0.72 4.29087845387e+11 7.15146409276e+12 +37 0.74 3.08855637556e+11 5.00846980094e+12 +38 0.76 2.24270970425e+11 3.54112058818e+12 +39 0.78 1.64210505205e+11 2.52631546702e+12 +40 0.8 1.2118708117e+11 1.81780621971e+12 +41 0.82 90109367359.1 1.31867367068e+12 +42 0.84 67481501334.4 9.64021449503e+11 +43 0.86 50880896383.4 7.09965997788e+11 +44 0.88 38613938681.2 5.26553710913e+11 +45 0.9 29486692086.8 3.93155896009e+11 +46 0.92 22650731882.4 2.95444330322e+11 +47 0.94 17498544395.3 2.23385674464e+11 +48 0.96 13591937526.4 1.69899220331e+11 +49 0.98 10612635712.6 1.29950642555e+11 +50 1.0 8327912706.34 99934953582.6 +51 1.02 6566502316.69 77252969474.2 +52 1.04 5201589672.36 60018343356.8 +53 1.06 4138717434.11 46853405843.3 +54 1.08 3307128665.58 36745874940.0 +55 1.1 2653529579.27 28947596241.1 +56 1.12 2137567708.15 22902511945.9 +57 1.14 1728534024.3 18195095739.0 +58 1.16 1402943799.0 14513212422.1 +59 1.18 1142752163.37 11621209113.9 +60 1.2 934030766.093 9340308300.6 +61 1.22 765981286.774 7534242773.65 +62 1.24 630196371.787 6098675145.29 +63 1.26 520103253.414 4953364870.6 +64 1.28 430542934.103 4036340534.04 +65 1.3 357450462.101 3299543229.91 +66 1.32 297610947.802 2705554551.18 +67 1.34 248472587.186 2225128105.44 +68 1.36 208002782.573 1835319108.76 +69 1.38 174576985.011 1518061159.35 +70 1.4 146892484.084 1259078837.33 +71 1.42 123901294.937 1047053582.16 +72 1.44 104757721.536 872981382.419 +73 1.46 88777241.639 729676313.267 +74 1.48 75404158.02 611385405.387 +75 1.5 64186061.7033 513488820.507 +76 1.52 54753607.1486 432265633.695 +77 1.54 46804443.7318 364710253.134 +78 1.56 40090410.0598 308388060.159 +79 1.58 34407297.9713 261321529.95 +80 1.6 29586646.6744 221900119.2 +81 1.62 25489145.661 188808745.634 +82 1.64 21999316.2868 160970856.824 +83 1.66 19021212.5921 137502982.517 +84 1.68 16474936.8715 117678352.86 +85 1.7 14293808.3245 100897694.735 +86 1.72 12422056.6082 86665727.6626 +87 1.74 10812938.3788 74572197.8496 +88 1.76 9427195.57103 64276535.39 +89 1.78 8231790.46096 55495411.7777 +90 1.8 7198865.45512 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308970.999537 1584552.10475 +118 2.36 278972.551763 1418587.76828 +119 2.38 252103.765513 1271192.59046 +120 2.4 228015.837009 1140158.32224 +121 2.42 206401.282366 1023554.60663 +122 2.44 186988.75765 919692.114521 +123 2.46 169538.563484 827090.818108 +124 2.48 153838.739168 744452.651831 +125 2.5 139701.665073 670637.92543 +126 2.52 126961.103835 604644.949624 +127 2.54 115469.620781 545592.416037 +128 2.56 105096.332511 492704.141327 +129 2.58 95724.9397832 445295.843157 +130 2.6 87252.0069441 402763.664479 +131 2.62 79585.4554502 364574.203947 +132 2.64 72643.2434671 330255.845328 +133 2.66 66352.2073932 299391.208536 +134 2.68 60647.0444312 271610.570248 +135 2.7 55469.4181565 246586.123584 +136 2.72 50767.1714483 224026.964698 +137 2.74 46493.633237 203674.709811 +138 2.76 42607.0073083 185299.659567 +139 2.78 39069.8329526 168697.439095 +140 2.8 35848.5085794 153686.051901 +141 2.82 32912.8705664 140103.294183 +142 2.84 30235.8206098 127804.483324 +143 2.86 27792.9956998 116660.460548 +144 2.88 25562.4755962 106555.833042 +145 2.9 23524.5233195 97387.4254387 +146 2.92 21661.3547409 89062.9145204 +147 2.94 19956.9338374 81499.6244039 +148 2.96 18396.7906059 74623.4624292 +149 2.98 16967.8589974 68367.9785194 +150 3.0 15658.3325568 62673.5329856 +151 3.02 14457.5357325 57486.5596649 +152 3.04 13355.809067 52758.912937 +153 3.06 12344.4066925 48447.2886046 +154 3.08 11415.4047444 44512.7098736 +155 3.1 10561.6194689 40920.0707567 +156 3.12 9776.5339459 37637.7301715 +157 3.14 9054.23247117 34637.1508274 +158 3.16 8389.34175838 31892.5777179 +159 3.18 7776.97821258 29380.7516608 +160 3.2 7212.7006167 27080.6538766 +161 3.22 6692.4676457 24973.2780793 +162 3.24 6212.59969004 23041.4269669 +163 3.26 5769.74452856 21269.5303734 +164 3.28 5360.84644195 19643.4826615 +165 3.3 4983.1184041 18150.4972204 +166 3.32 4634.01702836 16778.97618 +167 3.34 4311.21998136 15518.393672 +168 3.36 4012.60560869 14359.191159 +169 3.38 3736.23454428 13292.6835236 +170 3.4 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b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.min @@ -0,0 +1,28 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# Optional: Make sure the pairwise energies look reasonable: +#pair_write 2 2 1001 r 2.6 16.0 test_tail-tail.dat t-t 0 0 +#pair_write 2 3 1001 r 2.6 16.0 test_tail-head.dat t-h 0 0 +#pair_write 1 2 1001 r 2.6 16.0 test_int-tail.dat i-t 0 0 +#pair_write 1 1 2573 r 2.6 16.0 test_int-int.dat i-i 0 0 +#pair_write 1 3 1001 r 2.6 16.0 test_int-head.dat i-h 0 0 +#pair_write 3 3 1001 r 2.6 16.0 test_head-head.dat h-h 0 0 + + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.npt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.npt new file mode 100644 index 000000000..bd86869ab --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.npt @@ -0,0 +1,57 @@ +# -------- REQUIREMENTS: --------- +# 1) This example may require additional features and bug fixes for LAMMPS. +# Be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 2) Unpack it +# 3) copy the .cpp and .h files to the src folding of your lammps installation. +# 4) Compile LAMMPS. +# +# (If LAMMPS complains about an "Invalid pair_style" +# then you made a mistake in the instructions above.) +# + +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 6.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs +dump 1 all custom 5000 traj_npt.lammpstrj id mol type x y z ix iy iz + + +thermo_style custom step temp pe etotal vol epair ebond eangle +thermo 1000 # time interval for printing out "thermo" data + + +fix fxlan all langevin 300.0 300.0 120 48279 +fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy + + +# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon +# for the "epsilon" used by the coarse-grained lipid. +# Note: The langevin damping parameter "120" corresponds to +# the 0.12ps damping time used in Watson et. al JCP 2011. +# Note: We maintain the system system at constant (zero) tention +# using a barostat damping parameter Pdamp=1000 ("0 0 1000") + + +# optional (not sure if this helps): +# balance x uniform y uniform + + +#restart 1000000 + +run 2000000 + +write_restart system_after_npt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.nvt new file mode 100644 index 000000000..775c074c2 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.nvt @@ -0,0 +1,53 @@ +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Normally, I would minimize the system and equilibrate the system at constant +# pressure and temperature beforehand. If you run lammps with "run.in.npt", +# it will generate a restart file "system_after_npt.rst" with reasonable +# coordinates at that temperature and pressure. Then we could load it now: +# +#read_restart system_after_npt.rst +# +# Unfortunately the LAMMPS "read_restart" command has been undependable over +# the past year (2012), and I feel it is safer to remove it from the examples. +# Instead, for this example, I just read the raw coordinates generated by +# moltemplate (and the default volume). (I get fewer questions this way.) +# However you should never run any liquid simulations at constant volume without +# pressure equilibration first. Hopefully in the future "read_restart" will +# work. Until then, try "read_dump", "dump2data.py", or "restart2data". + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +timestep 6.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs +dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz + + +thermo_style custom step temp pe etotal vol epair ebond eangle +thermo 1000 # time interval for printing out "thermo" data + + +fix fxlan all langevin 300.0 300.0 120 48279 +fix fxnve all nve + +# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB. +# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon. +# Note: The langevin damping parameter "120" corresponds to +# the 0.12ps damping time used in Watson et. al JCP 2011. + +#restart 1000000 + +run 1000000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/README.TXT new file mode 100644 index 000000000..31abcd66e --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/README.TXT @@ -0,0 +1,33 @@ +# This directory contains examples of how to run a short simulation of a +# coarse-grained protein-like polymer, folding in the presence and absence of +# a chaperone (modeled as an attractive or repulsie spherical shell). +# +# The protein models and the chaperone models are described and used here: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) +# ...and also here: +# AI Jewett and J-E Shea, J. Mol. Biol, Vol 363(5), (2006) +# +# (In the "frustrated+minichaperone" directory, the protein is +# placed outside the chaperone sphere, as opposed to inside.) +# +# -------- REQUIREMENTS: --------- +# 1) These examples require the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) They also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. +# + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files in each directory. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT new file mode 100644 index 000000000..a52f73ff7 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT @@ -0,0 +1,32 @@ +# This directory demonstrates how to run a long simulation of +# the "frustrated" coarse-grained protein confined in a frustrated +# coarse-grained chaperonin (R=6, h=0.475) as described in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) +# +# Note: If you want to use a "hydrophilic" chaperone (with h=0.0 +# instead of h=0.475), then replace the word "CHAP_INTERIOR_H0.475" +# (at the end of "system.lt") with "CHAP_INTERIOR_H0" +# +# Because this process takes a long time (even with the help of the chaperone) +# I save the data relatively infrequently. +# +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh new file mode 100755 index 000000000..45bd2d451 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh @@ -0,0 +1,31 @@ +# You would probably run lammps this way: +# +# lmp_ubuntu -i run.in.nvt + +# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer +# to the input scripts & data files you created earlier when you ran moltemplate +# system.in.init, system.in.settings, system.data + + + + +# ----------------------------------- + + + +LAMMPS_COMMAND="lmp_ubuntu" + +# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. + +# Run lammps using the following 3 commands: + +"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +"$LAMMPS_COMMAND" -i run.in.nvt # production run + +# Alternately, if you have MPI installed, try something like this: + +#NUMPROCS=4 +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh new file mode 100755 index 000000000..f2462426f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh @@ -0,0 +1,24 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -overlay-dihdedrals system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + cp -r table*.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt new file mode 100644 index 000000000..019afc144 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 000000000..9e34246f8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,86 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 28 !NATOM + 1 1 2 2 0.000000 1.0000 0 + 2 1 1 1 0.000000 1.0000 0 + 3 1 2 2 0.000000 1.0000 0 + 4 1 1 1 0.000000 1.0000 0 + 5 1 2 2 0.000000 1.0000 0 + 6 1 1 1 0.000000 1.0000 0 + 7 1 3 3 0.000000 1.0000 0 + 8 1 3 3 0.000000 1.0000 0 + 9 1 1 1 0.000000 1.0000 0 + 10 1 2 2 0.000000 1.0000 0 + 11 1 1 1 0.000000 1.0000 0 + 12 1 2 2 0.000000 1.0000 0 + 13 1 1 1 0.000000 1.0000 0 + 14 1 2 2 0.000000 1.0000 0 + 15 1 3 3 0.000000 1.0000 0 + 16 1 3 3 0.000000 1.0000 0 + 17 1 3 3 0.000000 1.0000 0 + 18 1 1 1 0.000000 1.0000 0 + 19 1 1 1 0.000000 1.0000 0 + 20 1 2 2 0.000000 1.0000 0 + 21 1 2 2 0.000000 1.0000 0 + 22 1 1 1 0.000000 1.0000 0 + 23 1 1 1 0.000000 1.0000 0 + 24 1 2 2 0.000000 1.0000 0 + 25 1 2 2 0.000000 1.0000 0 + 26 1 1 1 0.000000 1.0000 0 + 27 1 2 2 0.000000 1.0000 0 + 28 2 4 4 0.000000 100.0000 0 + + 26 !NBOND: bonds + 1 2 2 3 3 4 4 5 + 5 6 6 7 7 8 8 9 + 9 10 10 11 11 12 12 13 + 13 14 14 15 15 16 16 17 + 17 18 18 19 19 20 20 21 + 21 22 22 23 23 24 24 25 + 25 26 26 27 + + 25 !NTHETA: angles + 13 14 15 7 8 9 6 7 8 + 16 17 18 15 16 17 2 3 4 + 4 5 6 9 10 11 11 12 13 + 14 15 16 1 2 3 3 4 5 + 10 11 12 12 13 14 25 26 27 + 5 6 7 8 9 10 17 18 19 + 18 19 20 22 23 24 21 22 23 + 19 20 21 20 21 22 23 24 25 + 24 25 26 + + 19 !NPHI: dihedrals + 1 2 3 4 2 3 4 5 + 3 4 5 6 4 5 6 7 + 8 9 10 11 9 10 11 12 + 10 11 12 13 11 12 13 14 + 12 13 14 15 15 16 17 18 + 16 17 18 19 17 18 19 20 + 18 19 20 21 19 20 21 22 + 20 21 22 23 21 22 23 24 + 22 23 24 25 23 24 25 26 + 24 25 26 27 + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg new file mode 100644 index 000000000..31853cd5a Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg new file mode 100644 index 000000000..fdc5c890b Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt new file mode 100644 index 000000000..e43026ba9 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt @@ -0,0 +1,216 @@ +# This file defines the "frustrated" coarse-grained protein model used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) + + +1beadFrustrated { + + # There are 3 atom types (referred to above as B, L, and N) + # Define their masses: + + write_once("Data Masses") { + @atom:B 1.0 + @atom:L 1.0 + @atom:N 1.0 + } + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679 + $atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341 + $atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966 + $atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709 + $atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737 + $atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098 + $atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919 + $atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901 + $atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617 + $atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043 + $atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721 + $atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951 + $atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019 + $atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217 + $atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429 + $atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711 + $atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358 + $atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719 + $atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014 + $atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053 + $atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748 + $atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224 + $atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255 + $atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346 + $atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166 + $atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097 + $atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463 + } + + # bond-ID bond-Type atom-ID atom-ID + + write('Data Bonds') { + $bond:b1 @bond:backbone $atom:a1 $atom:a2 + $bond:b2 @bond:backbone $atom:a2 $atom:a3 + $bond:b3 @bond:backbone $atom:a3 $atom:a4 + $bond:b4 @bond:backbone $atom:a4 $atom:a5 + $bond:b5 @bond:backbone $atom:a5 $atom:a6 + $bond:b6 @bond:backbone $atom:a6 $atom:a7 + $bond:b7 @bond:backbone $atom:a7 $atom:a8 + $bond:b8 @bond:backbone $atom:a8 $atom:a9 + $bond:b9 @bond:backbone $atom:a9 $atom:a10 + $bond:b10 @bond:backbone $atom:a10 $atom:a11 + $bond:b11 @bond:backbone $atom:a11 $atom:a12 + $bond:b12 @bond:backbone $atom:a12 $atom:a13 + $bond:b13 @bond:backbone $atom:a13 $atom:a14 + $bond:b14 @bond:backbone $atom:a14 $atom:a15 + $bond:b15 @bond:backbone $atom:a15 $atom:a16 + $bond:b16 @bond:backbone $atom:a16 $atom:a17 + $bond:b17 @bond:backbone $atom:a17 $atom:a18 + $bond:b18 @bond:backbone $atom:a18 $atom:a19 + $bond:b19 @bond:backbone $atom:a19 $atom:a20 + $bond:b20 @bond:backbone $atom:a20 $atom:a21 + $bond:b21 @bond:backbone $atom:a21 $atom:a22 + $bond:b22 @bond:backbone $atom:a22 $atom:a23 + $bond:b23 @bond:backbone $atom:a23 $atom:a24 + $bond:b24 @bond:backbone $atom:a24 $atom:a25 + $bond:b25 @bond:backbone $atom:a25 $atom:a26 + $bond:b26 @bond:backbone $atom:a26 $atom:a27 + } + + # (3-body) Angles are specified below + + # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. + # (These interactions are not determined by atom type.) + + # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID + + write('Data Dihedrals') { + + $dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7 + + # Dihedral angle forces in the turn regions were switched off + # (in this model) so just I comment them out (and \ the variable names). + # \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8 + # \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9 + # \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10 + + $dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15 + + # Dihedral angle forces in the turn regions were switched off + # (in this model) so just I comment them out (and \ the variable names). + # \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16 + # \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17 + + $dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27 + } + + # All consecutively bonded triplets of atoms same 3-body bond-angle + # interaction parameters. Of coarse, we could specify them all explicitly + # (as we did for the dihedrals above), but I wanted to show how to specify + # angles by atom type instead. (You can do this for dihedrals & impropers + # also.) + + # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type + + write_once('Data Angles By Type') { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # (The "*" is a wildcard character. I use "*" to denote any atom-type or + # bond-type which is defined within the current namespace: 1beadFrustrated) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 + pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 + pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 + } + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond-Type bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 100.0 1.0 + } + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # angle-Type anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 13.3333333333 105.0 + } + + + # We use tabular dihedral potentials to implement the dihedral forces. + # (Actually there is a way to use Fourier series, using multiple charmm + # style dihedral interactions, but it's slower and messier.) + + write_once("In Settings") { + # style file keyword + dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA + dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA + # No need to specify dihedral interactions in the turn regions. (none exist) + } + + write_once("In Settings") { + # Optional: define the atoms in the "proteins" group + group proteins type @atom:B + group proteins type @atom:L + group proteins type @atom:N + } + + # LAMMPS has many available force field styles (and atom styles). + # Here, we pick the ones which work well for this molecular model: + + write_once("In Init") { + # --- Default options for the "1BeadFrustrated" protein model --- + # --- (These can be overridden later.) --- + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid table spline 360 + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + +} # 1beadFrustrated + + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt new file mode 100644 index 000000000..54e2de437 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt @@ -0,0 +1,85 @@ +import "1beadFrustrated.lt" + + +# Alternate starting conformation (same molecule): + + +1beadMisfolded inherits 1beadFrustrated { + + # This molecule "inherits" all of its features from "1beadFrustrated". + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876 + $atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251 + $atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085 + $atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451 + $atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135 + $atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977 + $atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409 + $atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275 + $atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938 + $atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398 + $atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186 + $atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916 + $atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704 + $atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331 + $atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056 + $atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167 + $atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633 + $atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523 + $atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791 + $atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346 + $atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555 + $atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946 + $atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493 + $atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934 + $atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086 + $atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181 + $atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868 + } + +} # 1beadMisfolded + + +1beadUnfolded inherits 1beadFrustrated { + + # This molecule "inherits" all of its features from "1beadFrustrated" + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 + $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 + $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 + $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 + $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 + $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 + $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 + $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 + $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 + $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 + $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 + $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 + $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 + $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 + $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 + $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 + $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 + $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 + $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 + $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 + $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 + $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 + $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 + $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 + $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 + $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 + $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 + } + +} # 1beadUnfolded + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt new file mode 100644 index 000000000..8266d2a89 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt @@ -0,0 +1,41 @@ +# Here we define a trivial molecule containing only one particle. + +Chaperonin { + + # atomID molID atomType charge x y z + + write("Data Atoms") { + $atom:C $mol @atom:C 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:C 100.0 + } + + write_once("In Settings") { + # If for some reason there are multiple chaperones present, + # I assume that they interact repulsively (hence, L=0) + # i j epsilon sigma K L + + pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 6.0 1 0 + + # Optional: define the atoms in the "chaperonins" group: + # (Defining a group for the chaperone makes it easy to immobilize it later.) + + group chaperonins type @atom:C + } + + + # Specify which pair_styles, and atom styles work well with + # this model. (Again this can be overridden later.) + + write_once("In Init") { + units lj + atom_style full + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 11.0 12.0 + } + +} # Chaperonin + +# We have not specified how this particle interacts with other particles +# besides itself. Later on you must do this. diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py new file mode 100755 index 000000000..9b86809cc --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py @@ -0,0 +1,87 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between atoms in the +# protein and a chaperone provided in the supplemental materials section of: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# This is stored in a tabulated force field with a singularity at a distance R. +# +# To calculate the table for interaction between +# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181 +# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181 +# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True +# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True + +from math import * +import sys + +def U(r, eps, sigma, R, h): + #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h)) + # Formula is undefined at r=0, but you can take the limit: + if r <= 0: + return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0) + - h*pow((sigma/R), 6.0)) + xp = sigma/(r+R) + xm = sigma/(r-R) + term10 = pow(xm, 10.0) - pow(xp, 10.0) + term4 = pow(xm, 4.0) - pow(xp, 4.0) + return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4) + +def F(r, eps, sigma, R, h): + # Formula is undefined at r=0, but you can take the limit: + if r <= 0: + return 0.0 + product_term_a = U(r, eps, sigma, R, h) / r + ixp = (r+R)/sigma + ixm = (r-R)/sigma + dix_dr = 1.0/sigma + term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0)) + term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0)) + product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4) + return product_term_a + product_term_b + + +class InputError(Exception): + """ A generic exception object containing a string for error reporting. + + """ + def __init__(self, err_msg): + self.err_msg = err_msg + def __str__(self): + return self.err_msg + def __repr__(self): + return str(self) + +if len(sys.argv) < 8: + sys.stderr.write("Error: expected 7 arguments:\n" + "\n" + "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n") + sys.exit(-1) + +epsilon = float(sys.argv[1]) +sigma = float(sys.argv[2]) +R = float(sys.argv[3]) +h = float(sys.argv[4]) +rmin = float(sys.argv[5]) +rmax = float(sys.argv[6]) +N = int(sys.argv[7]) + +subtract_Urcut = False +if len(sys.argv) == 9: + subtract_Urcut = True +rcut = rmax + +for i in range(0,N): + r = rmin + i*(rmax-rmin)/(N-1) + U_r = U(r, epsilon, sigma, R, h) + F_r = F(r, epsilon, sigma, R, h) + if subtract_Urcut: + U_r -= U(rcut, epsilon, sigma, R, h) + if (r >= rcut) or (i==N-1): + U_r = 0.0 + F_r = 0.0 + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py new file mode 100755 index 000000000..34c66418a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py @@ -0,0 +1,67 @@ +#!/usr/bin/env python + +# Calculate a table of dihedral angle interactions used in the alpha-helix +# and beta-sheet regions of the frustrated protein model described in +# provided in figure 8 of the supplemental materials section of: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# Note that the "A" and "B" parameters were incorrectly reported to be +# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon. +# The phiA and phiB values were 57.29577951308232 degrees (1 rad) +# and 180 degrees, respectively. Both expA and expB were 6.0. +# +# To generate the table used for the alpha-helix (1 degree resolution) use this: +# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 +# To generate the table used for the beta-sheets (1 degree resolution) use this: +# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 +# +# (If you're curious as to why I set the location of the minima at phi_alpha +# to 1.0 radians (57.2957795 degrees), there was no particularly good reason. +# I think the correct value turns out to be something closer to 50 degrees.) + + +from math import * +import sys + + +# The previous version included the repulsive core term +def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False): + conv_units = pi/180.0 + if use_radians: + conv_units = 1.0 + termA = pow(cos(0.5*(phi-phiA)*conv_units), expA) + termB = pow(cos(0.5*(phi-phiB)*conv_units), expB) + return -A*termA - B*termB + +# The previous version included the repulsive core term +def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False): + conv_units = pi/180.0 + if use_radians: + conv_units = 1.0 + termA = (0.5*sin(0.5*(phi-phiA)*conv_units) * + expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0)) + termB = (0.5*sin(0.5*(phi-phiB)*conv_units) * + expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0)) + return -conv_units*(A*termA + B*termB) + +if len(sys.argv) != 10: + sys.stderr.write("Error: expected 9 arguments:\n" + "\n" + "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n") + sys.exit(-1) + +A = float(sys.argv[1]) +phiA = float(sys.argv[2]) +expA = float(sys.argv[3]) +B = float(sys.argv[4]) +phiB = float(sys.argv[5]) +expB = float(sys.argv[6]) +phi_min = float(sys.argv[7]) +phi_max = float(sys.argv[8]) +N = int(sys.argv[9]) + +for i in range(0,N): + phi = phi_min + i*(phi_max - phi_min)/(N-1) + U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False) + F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False) + print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt new file mode 100644 index 000000000..d70ea9b1f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt @@ -0,0 +1,45 @@ +write_once("Data Boundary") { + 0.0 20.0 xlo xhi + 0.0 20.0 ylo yhi + 0.0 20.0 zlo zhi +} + + +import "1beadFrustrated_variants.lt" +import "chaperonin.lt" + + +protein = new 1beadMisfolded # (frustrated protein, misfolded conformation) +chaperinin = new Chaperonin # (hollow chaperonin cavity. usually immobile) + + + +# ---- Now define interactions between the atoms in the protein ---- +# ---- (named "B", "L", "N") and the atom which represents the ---- +# ---- chaperone ("C"). These interactions are tabulated. ---- + +write_once("In Settings") { + pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/B table table_chaperonin_h=0.475.dat CH_H0.475 + pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/L table table_chaperonin_h=0.dat CH_H0 + pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/N table table_chaperonin_h=0.dat CH_H0 +} + +# Note: If you want to use a "hydrophilic" chaperone (with h=0, not h=0.475) +# then replace "table_chaperonin_h=0_475.dat CH_H0.475" +# with "table_chaperonin_h=0.dat CH_H0" + +# LAMMPS has many available force field styles (and atom styles). Here we +# select the ones which work well for the full combine system. (This should +# override any settings made in "1beadFrustrated.lt" or "chaperonin.lt") + + +write_once("In Init") { + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid table spline 360 + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 1181 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) +} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat new file mode 100644 index 000000000..675d228a9 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat @@ -0,0 +1,1188 @@ +# Interaction between a chaperonin wall and hydrophobic ("B") beads (h=0.475). +# LAMMPS would crash unless I set the minimum radius to a positive value (not 0) + +CH_H0.475 +N 1181 R 0.00000000001 5.9 + +1 0.00000000001 -0.018422088583 0.0 +2 0.005 -0.0184221525389 2.55824082873e-05 +3 0.01 -0.0184223444081 5.11654127471e-05 +4 0.015 -0.018422664195 7.67496107175e-05 +5 0.02 -0.0184231119071 0.000102335598797 +6 0.025 -0.018423687555 0.000127923973785 +7 0.03 -0.0184243911519 0.000153515332637 +8 0.035 -0.0184252227143 0.000179110272379 +9 0.04 -0.0184261822615 0.000204709390236 +10 0.045 -0.0184272698161 0.000230313283607 +11 0.05 -0.0184284854033 0.000255922550119 +12 0.055 -0.0184298290516 0.000281537787625 +13 0.06 -0.0184313007922 0.000307159594253 +14 0.065 -0.0184329006595 0.000332788568419 +15 0.07 -0.0184346286908 0.000358425308862 +16 0.075 -0.0184364849265 0.000384070414671 +17 0.08 -0.0184384694099 0.000409724485298 +18 0.085 -0.0184405821873 0.000435388120601 +19 0.09 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1277612.0471 -47109063.5591 +1148 5.735 1538935.10642 -57819017.4811 +1149 5.74 1860314.59485 -71242218.9505 +1150 5.745 2257134.5845 -88139540.3817 +1151 5.75 2749142.49547 -109506722.176 +1152 5.755 3361811.73098 -136653799.897 +1153 5.76 4128170.65016 -171313840.077 +1154 5.765 5091272.07333 -215792744.495 +1155 5.77 6307548.29223 -273176998.31 +1156 5.775 7851398.52158 -347623759.363 +1157 5.78 9821503.74726 -444768835.455 +1158 5.785 12349580.5127 -572304762.479 +1159 5.79 15612604.744 -740806327.342 +1160 5.795 19850012.3018 -964919124.004 +1161 5.8 25388097.1921 -1265085490.72 +1162 5.805 32674911.255 -1670073366.45 +1163 5.81 42330627.3386 -2220716617.13 +1164 5.815 55220893.742 -2975502155.22 +1165 5.82 72564721.5485 -4019002953.22 +1166 5.825 96094798.4335 -5474746758.15 +1167 5.83 128298297.388 -7525081897.32 +1168 5.835 172782757.396 -10442221387.6 +1169 5.84 234838762.891 -14637386017.7 +1170 5.845 322316442.616 -20739670704.4 +1171 5.85 447009526.718 -29724465089.5 +1172 5.855 626872755.056 -43125823862.6 +1173 5.86 889629660.718 -63393502739.0 +1174 5.865 1278740106.83 -94503868935.1 +1175 5.87 1863446791.23 -1.43025101229e+11 +1176 5.875 2756012237.96 -2.20012469835e+11 +1177 5.88 4141901662.1 -3.44454801129e+11 +1178 5.885 6333810219.82 -5.49690750348e+11 +1179 5.89 9870702215.02 -8.95661856872e+11 +1180 5.895 15704120493.1 -1.49296797827e+12 +1181 5.9 25558689542.6 -2.55153879404e+12 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat new file mode 100644 index 000000000..2ad6d7b69 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat @@ -0,0 +1,1187 @@ +# Interaction between a chaperonin wall and hydrophilic beads (type L or N, h=0) + +CH_H0 +N 1181 R 0.00000000001 5.9 + +1 0.00000000001 8.31299178857e-07 0.0 +2 0.005 8.31311879342e-07 -5.08022586688e-09 +3 0.01 8.31349981758e-07 -1.01608369733e-08 +4 0.015 8.31413488996e-07 -1.52422186449e-08 +5 0.02 8.31502405871e-07 -2.03247562721e-08 +6 0.025 8.31616739127e-07 -2.54088353865e-08 +7 0.03 8.31756497437e-07 -3.04948417048e-08 +8 0.035 8.319216914e-07 -3.55831611709e-08 +9 0.04 8.32112333547e-07 -4.06741800058e-08 +10 0.045 8.32328438343e-07 -4.57682847516e-08 +11 0.05 8.32570022183e-07 -5.08658623183e-08 +12 0.055 8.328371034e-07 -5.59673000292e-08 +13 0.06 8.33129702263e-07 -6.10729856679e-08 +14 0.065 8.33447840983e-07 -6.61833075238e-08 +15 0.07 8.33791543713e-07 -7.12986544391e-08 +16 0.075 8.34160836552e-07 -7.64194158551e-08 +17 0.08 8.34555747546e-07 -8.15459818584e-08 +18 0.085 8.34976306696e-07 -8.66787432278e-08 +19 0.09 8.35422545957e-07 -9.18180914814e-08 +20 0.095 8.35894499243e-07 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--- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_dihedral_frustrated.dat @@ -0,0 +1,735 @@ +# Table of the potential and its negative derivative for frustrated alpha helix +# (Note: Derivatives are in units of energy/radians, not energy/degrees.) +# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 + +FRUSTRATED_ALPHA +N 360 DEGREES + +1 0.0 -2.74081145103 0.0783990792662 +2 1.0 -2.81950869101 0.0789852583442 +3 2.0 -2.89876136749 0.0795096391909 +4 3.0 -2.97850675562 0.0799703813963 +5 4.0 -3.05868032959 0.0803657243943 +6 5.0 -3.13921584545 0.0806939935737 +7 6.0 -3.22004543014 0.0809536062381 +8 7.0 -3.30109967628 0.0811430773977 +9 8.0 -3.38230774267 0.0812610253741 +10 9.0 -3.46359746038 0.0813061772009 +11 10.0 -3.54489544401 0.0812773738039 +12 11.0 -3.62612720812 0.0811735749433 +13 12.0 -3.70721728841 0.0809938639029 +14 13.0 -3.78808936748 0.080737451911 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-1.53878331313 0.061018148454 +345 344.0 -1.60045794659 0.0623272072653 +346 345.0 -1.66342954101 0.0636117049668 +347 346.0 -1.72767243359 0.0648694329207 +348 347.0 -1.79315873807 0.0660981537565 +349 348.0 -1.85985831882 0.0672956071568 +350 349.0 -1.92773877092 0.0684595158069 +351 350.0 -1.99676540616 0.0695875914917 +352 351.0 -2.06690124527 0.0706775413231 +353 352.0 -2.13810701636 0.0717270740805 +354 353.0 -2.21034115987 0.0727339066469 +355 354.0 -2.28355983986 0.0736957705223 +356 355.0 -2.35771696194 0.0746104183955 +357 356.0 -2.43276419776 0.0754756307561 +358 357.0 -2.50865101613 0.0762892225281 +359 358.0 -2.58532472075 0.0770490497051 +360 359.0 -2.66273049463 0.0777530159679 + +# Table of the potential and its negative derivative for frustrated beta sheet +# (Note: Derivatives are in units of energy/radians, not energy/degrees.) +# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 + +FRUSTRATED_BETA +N 360 DEGREES + +1 0.0 -2.55809068762 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0.0704439199439 +358 357.0 -2.3414076153 0.0712032738621 +359 358.0 -2.41296973939 0.0719124463259 +360 359.0 -2.48521512832 0.072569481568 diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min new file mode 100644 index 000000000..321ba3c09 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min @@ -0,0 +1,25 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# Optional: Make sure the pairwise energies look reasonable: +pair_write 1 4 1001 r 0.00000000001 5.05 test_chap-B.dat C-B 0 0 +pair_write 2 4 1001 r 0.00000000001 5.05 test_chap-L.dat C-L 0 0 +pair_write 3 4 1001 r 0.00000000001 5.05 test_chap-N.dat C-N 0 0 + + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt new file mode 100644 index 000000000..7c0855cb8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt @@ -0,0 +1,48 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.025 +dump 1 all custom 50000 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +# Keep the chaperonin fixed. Only let the protein move. + +fix fxlan proteins langevin 0.25 0.25 1.0 48279 +fix fxnve proteins nve + +# Notes: +# The temperature is in reduced units and is set to 0.25 +# which is the folding temperature for the frustrated protein +# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, +# as it was in the paper. (Hopefully folding times should be similar.) +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 50000 #(time interval for printing out "thermo" data) + +#restart 100000000 restart_nvt + +run 1000000000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT new file mode 100644 index 000000000..ecb9adad2 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT @@ -0,0 +1,38 @@ +# This directory demonstrates how to run a long simulation of +# the "frustrated" coarse-grained protein in the presence of one +# or more coarse-graine small ("mini") chaperones (R=3, h=0.6) as described in: +# +# AI Jewett and J-E Shea, J. Mol. Biol, Vol 363(5), (2006) +# and earlier in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# +# Because this process takes a long time (even with the help of the chaperone) +# I save the data relatively infrequently. +# +# Note: In the 2006 paper, only one protein and one chaperone was simulated. +# In this example, 8 proteins and 8 chaperones were simulated. +# +# Note: In this case, the chaperones appear to catalyze aggregation. +# This is due to an artifact in the protein model. That model +# was not designed to study aggregation. However the simulation +# is suitable for making pretty pictures (to show off moltemplate). +# +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh new file mode 100755 index 000000000..45bd2d451 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh @@ -0,0 +1,31 @@ +# You would probably run lammps this way: +# +# lmp_ubuntu -i run.in.nvt + +# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer +# to the input scripts & data files you created earlier when you ran moltemplate +# system.in.init, system.in.settings, system.data + + + + +# ----------------------------------- + + + +LAMMPS_COMMAND="lmp_ubuntu" + +# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. + +# Run lammps using the following 3 commands: + +"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +"$LAMMPS_COMMAND" -i run.in.nvt # production run + +# Alternately, if you have MPI installed, try something like this: + +#NUMPROCS=4 +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh new file mode 100755 index 000000000..f2462426f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh @@ -0,0 +1,24 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -overlay-dihdedrals system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + cp -r table*.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt new file mode 100644 index 000000000..019afc144 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 000000000..b0013ccc6 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,476 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 224 !NATOM + 1 1 2 2 0.000000 1.0000 0 + 2 1 1 1 0.000000 1.0000 0 + 3 1 2 2 0.000000 1.0000 0 + 4 1 1 1 0.000000 1.0000 0 + 5 1 2 2 0.000000 1.0000 0 + 6 1 1 1 0.000000 1.0000 0 + 7 1 3 3 0.000000 1.0000 0 + 8 1 3 3 0.000000 1.0000 0 + 9 1 1 1 0.000000 1.0000 0 + 10 1 2 2 0.000000 1.0000 0 + 11 1 1 1 0.000000 1.0000 0 + 12 1 2 2 0.000000 1.0000 0 + 13 1 1 1 0.000000 1.0000 0 + 14 1 2 2 0.000000 1.0000 0 + 15 1 3 3 0.000000 1.0000 0 + 16 1 3 3 0.000000 1.0000 0 + 17 1 3 3 0.000000 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220 12 4 4 0.000000 100.0000 0 + 221 13 4 4 0.000000 100.0000 0 + 222 14 4 4 0.000000 100.0000 0 + 223 15 4 4 0.000000 100.0000 0 + 224 16 4 4 0.000000 100.0000 0 + + 208 !NBOND: bonds + 1 2 2 3 3 4 4 5 + 5 6 6 7 7 8 8 9 + 9 10 10 11 11 12 12 13 + 13 14 14 15 15 16 16 17 + 17 18 18 19 19 20 20 21 + 21 22 22 23 23 24 24 25 + 25 26 26 27 28 29 29 30 + 30 31 31 32 32 33 33 34 + 34 35 35 36 36 37 37 38 + 38 39 39 40 40 41 41 42 + 42 43 43 44 44 45 45 46 + 46 47 47 48 48 49 49 50 + 50 51 51 52 52 53 53 54 + 55 56 56 57 57 58 58 59 + 59 60 60 61 61 62 62 63 + 63 64 64 65 65 66 66 67 + 67 68 68 69 69 70 70 71 + 71 72 72 73 73 74 74 75 + 75 76 76 77 77 78 78 79 + 79 80 80 81 82 83 83 84 + 84 85 85 86 86 87 87 88 + 88 89 89 90 90 91 91 92 + 92 93 93 94 94 95 95 96 + 96 97 97 98 98 99 99 100 + 100 101 101 102 102 103 103 104 + 104 105 105 106 106 107 107 108 + 109 110 110 111 111 112 112 113 + 113 114 114 115 115 116 116 117 + 117 118 118 119 119 120 120 121 + 121 122 122 123 123 124 124 125 + 125 126 126 127 127 128 128 129 + 129 130 130 131 131 132 132 133 + 133 134 134 135 136 137 137 138 + 138 139 139 140 140 141 141 142 + 142 143 143 144 144 145 145 146 + 146 147 147 148 148 149 149 150 + 150 151 151 152 152 153 153 154 + 154 155 155 156 156 157 157 158 + 158 159 159 160 160 161 161 162 + 163 164 164 165 165 166 166 167 + 167 168 168 169 169 170 170 171 + 171 172 172 173 173 174 174 175 + 175 176 176 177 177 178 178 179 + 179 180 180 181 181 182 182 183 + 183 184 184 185 185 186 186 187 + 187 188 188 189 190 191 191 192 + 192 193 193 194 194 195 195 196 + 196 197 197 198 198 199 199 200 + 200 201 201 202 202 203 203 204 + 204 205 205 206 206 207 207 208 + 208 209 209 210 210 211 211 212 + 212 213 213 214 214 215 215 216 + + 200 !NTHETA: angles + 13 14 15 40 41 42 67 68 69 + 94 95 96 121 122 123 148 149 150 + 175 176 177 202 203 204 7 8 9 + 6 7 8 16 17 18 34 35 36 + 33 34 35 43 44 45 61 62 63 + 60 61 62 70 71 72 88 89 90 + 87 88 89 97 98 99 115 116 117 + 114 115 116 124 125 126 142 143 144 + 141 142 143 151 152 153 169 170 171 + 168 169 170 178 179 180 196 197 198 + 195 196 197 205 206 207 15 16 17 + 42 43 44 69 70 71 96 97 98 + 123 124 125 150 151 152 177 178 179 + 204 205 206 2 3 4 4 5 6 + 9 10 11 11 12 13 29 30 31 + 31 32 33 36 37 38 38 39 40 + 56 57 58 58 59 60 63 64 65 + 65 66 67 83 84 85 85 86 87 + 90 91 92 92 93 94 110 111 112 + 112 113 114 117 118 119 119 120 121 + 137 138 139 139 140 141 144 145 146 + 146 147 148 164 165 166 166 167 168 + 171 172 173 173 174 175 191 192 193 + 193 194 195 198 199 200 200 201 202 + 14 15 16 41 42 43 68 69 70 + 95 96 97 122 123 124 149 150 151 + 176 177 178 203 204 205 1 2 3 + 3 4 5 10 11 12 12 13 14 + 25 26 27 28 29 30 30 31 32 + 37 38 39 39 40 41 52 53 54 + 55 56 57 57 58 59 64 65 66 + 66 67 68 79 80 81 82 83 84 + 84 85 86 91 92 93 93 94 95 + 106 107 108 109 110 111 111 112 113 + 118 119 120 120 121 122 133 134 135 + 136 137 138 138 139 140 145 146 147 + 147 148 149 160 161 162 163 164 165 + 165 166 167 172 173 174 174 175 176 + 187 188 189 190 191 192 192 193 194 + 199 200 201 201 202 203 214 215 216 + 5 6 7 8 9 10 32 33 34 + 35 36 37 59 60 61 62 63 64 + 86 87 88 89 90 91 113 114 115 + 116 117 118 140 141 142 143 144 145 + 167 168 169 170 171 172 194 195 196 + 197 198 199 17 18 19 44 45 46 + 71 72 73 98 99 100 125 126 127 + 152 153 154 179 180 181 206 207 208 + 18 19 20 22 23 24 21 22 23 + 45 46 47 49 50 51 48 49 50 + 72 73 74 76 77 78 75 76 77 + 99 100 101 103 104 105 102 103 104 + 126 127 128 130 131 132 129 130 131 + 153 154 155 157 158 159 156 157 158 + 180 181 182 184 185 186 183 184 185 + 207 208 209 211 212 213 210 211 212 + 19 20 21 20 21 22 23 24 25 + 24 25 26 46 47 48 47 48 49 + 50 51 52 51 52 53 73 74 75 + 74 75 76 77 78 79 78 79 80 + 100 101 102 101 102 103 104 105 106 + 105 106 107 127 128 129 128 129 130 + 131 132 133 132 133 134 154 155 156 + 155 156 157 158 159 160 159 160 161 + 181 182 183 182 183 184 185 186 187 + 186 187 188 208 209 210 209 210 211 + 212 213 214 213 214 215 + + 152 !NPHI: dihedrals + 1 2 3 4 2 3 4 5 + 3 4 5 6 4 5 6 7 + 8 9 10 11 9 10 11 12 + 10 11 12 13 11 12 13 14 + 12 13 14 15 15 16 17 18 + 16 17 18 19 17 18 19 20 + 18 19 20 21 19 20 21 22 + 20 21 22 23 21 22 23 24 + 22 23 24 25 23 24 25 26 + 24 25 26 27 28 29 30 31 + 29 30 31 32 30 31 32 33 + 31 32 33 34 35 36 37 38 + 36 37 38 39 37 38 39 40 + 38 39 40 41 39 40 41 42 + 42 43 44 45 43 44 45 46 + 44 45 46 47 45 46 47 48 + 46 47 48 49 47 48 49 50 + 48 49 50 51 49 50 51 52 + 50 51 52 53 51 52 53 54 + 55 56 57 58 56 57 58 59 + 57 58 59 60 58 59 60 61 + 62 63 64 65 63 64 65 66 + 64 65 66 67 65 66 67 68 + 66 67 68 69 69 70 71 72 + 70 71 72 73 71 72 73 74 + 72 73 74 75 73 74 75 76 + 74 75 76 77 75 76 77 78 + 76 77 78 79 77 78 79 80 + 78 79 80 81 82 83 84 85 + 83 84 85 86 84 85 86 87 + 85 86 87 88 89 90 91 92 + 90 91 92 93 91 92 93 94 + 92 93 94 95 93 94 95 96 + 96 97 98 99 97 98 99 100 + 98 99 100 101 99 100 101 102 + 100 101 102 103 101 102 103 104 + 102 103 104 105 103 104 105 106 + 104 105 106 107 105 106 107 108 + 109 110 111 112 110 111 112 113 + 111 112 113 114 112 113 114 115 + 116 117 118 119 117 118 119 120 + 118 119 120 121 119 120 121 122 + 120 121 122 123 123 124 125 126 + 124 125 126 127 125 126 127 128 + 126 127 128 129 127 128 129 130 + 128 129 130 131 129 130 131 132 + 130 131 132 133 131 132 133 134 + 132 133 134 135 136 137 138 139 + 137 138 139 140 138 139 140 141 + 139 140 141 142 143 144 145 146 + 144 145 146 147 145 146 147 148 + 146 147 148 149 147 148 149 150 + 150 151 152 153 151 152 153 154 + 152 153 154 155 153 154 155 156 + 154 155 156 157 155 156 157 158 + 156 157 158 159 157 158 159 160 + 158 159 160 161 159 160 161 162 + 163 164 165 166 164 165 166 167 + 165 166 167 168 166 167 168 169 + 170 171 172 173 171 172 173 174 + 172 173 174 175 173 174 175 176 + 174 175 176 177 177 178 179 180 + 178 179 180 181 179 180 181 182 + 180 181 182 183 181 182 183 184 + 182 183 184 185 183 184 185 186 + 184 185 186 187 185 186 187 188 + 186 187 188 189 190 191 192 193 + 191 192 193 194 192 193 194 195 + 193 194 195 196 197 198 199 200 + 198 199 200 201 199 200 201 202 + 200 201 202 203 201 202 203 204 + 204 205 206 207 205 206 207 208 + 206 207 208 209 207 208 209 210 + 208 209 210 211 209 210 211 212 + 210 211 212 213 211 212 213 214 + 212 213 214 215 213 214 215 216 + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg new file mode 100644 index 000000000..c62a881b2 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg new file mode 100644 index 000000000..38ef54396 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt new file mode 100644 index 000000000..e43026ba9 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt @@ -0,0 +1,216 @@ +# This file defines the "frustrated" coarse-grained protein model used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) + + +1beadFrustrated { + + # There are 3 atom types (referred to above as B, L, and N) + # Define their masses: + + write_once("Data Masses") { + @atom:B 1.0 + @atom:L 1.0 + @atom:N 1.0 + } + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679 + $atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341 + $atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966 + $atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709 + $atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737 + $atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098 + $atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919 + $atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901 + $atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617 + $atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043 + $atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721 + $atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951 + $atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019 + $atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217 + $atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429 + $atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711 + $atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358 + $atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719 + $atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014 + $atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053 + $atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748 + $atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224 + $atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255 + $atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346 + $atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166 + $atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097 + $atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463 + } + + # bond-ID bond-Type atom-ID atom-ID + + write('Data Bonds') { + $bond:b1 @bond:backbone $atom:a1 $atom:a2 + $bond:b2 @bond:backbone $atom:a2 $atom:a3 + $bond:b3 @bond:backbone $atom:a3 $atom:a4 + $bond:b4 @bond:backbone $atom:a4 $atom:a5 + $bond:b5 @bond:backbone $atom:a5 $atom:a6 + $bond:b6 @bond:backbone $atom:a6 $atom:a7 + $bond:b7 @bond:backbone $atom:a7 $atom:a8 + $bond:b8 @bond:backbone $atom:a8 $atom:a9 + $bond:b9 @bond:backbone $atom:a9 $atom:a10 + $bond:b10 @bond:backbone $atom:a10 $atom:a11 + $bond:b11 @bond:backbone $atom:a11 $atom:a12 + $bond:b12 @bond:backbone $atom:a12 $atom:a13 + $bond:b13 @bond:backbone $atom:a13 $atom:a14 + $bond:b14 @bond:backbone $atom:a14 $atom:a15 + $bond:b15 @bond:backbone $atom:a15 $atom:a16 + $bond:b16 @bond:backbone $atom:a16 $atom:a17 + $bond:b17 @bond:backbone $atom:a17 $atom:a18 + $bond:b18 @bond:backbone $atom:a18 $atom:a19 + $bond:b19 @bond:backbone $atom:a19 $atom:a20 + $bond:b20 @bond:backbone $atom:a20 $atom:a21 + $bond:b21 @bond:backbone $atom:a21 $atom:a22 + $bond:b22 @bond:backbone $atom:a22 $atom:a23 + $bond:b23 @bond:backbone $atom:a23 $atom:a24 + $bond:b24 @bond:backbone $atom:a24 $atom:a25 + $bond:b25 @bond:backbone $atom:a25 $atom:a26 + $bond:b26 @bond:backbone $atom:a26 $atom:a27 + } + + # (3-body) Angles are specified below + + # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. + # (These interactions are not determined by atom type.) + + # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID + + write('Data Dihedrals') { + + $dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7 + + # Dihedral angle forces in the turn regions were switched off + # (in this model) so just I comment them out (and \ the variable names). + # \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8 + # \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9 + # \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10 + + $dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15 + + # Dihedral angle forces in the turn regions were switched off + # (in this model) so just I comment them out (and \ the variable names). + # \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16 + # \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17 + + $dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27 + } + + # All consecutively bonded triplets of atoms same 3-body bond-angle + # interaction parameters. Of coarse, we could specify them all explicitly + # (as we did for the dihedrals above), but I wanted to show how to specify + # angles by atom type instead. (You can do this for dihedrals & impropers + # also.) + + # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type + + write_once('Data Angles By Type') { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # (The "*" is a wildcard character. I use "*" to denote any atom-type or + # bond-type which is defined within the current namespace: 1beadFrustrated) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 + pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 + pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 + } + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond-Type bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 100.0 1.0 + } + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # angle-Type anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 13.3333333333 105.0 + } + + + # We use tabular dihedral potentials to implement the dihedral forces. + # (Actually there is a way to use Fourier series, using multiple charmm + # style dihedral interactions, but it's slower and messier.) + + write_once("In Settings") { + # style file keyword + dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA + dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA + # No need to specify dihedral interactions in the turn regions. (none exist) + } + + write_once("In Settings") { + # Optional: define the atoms in the "proteins" group + group proteins type @atom:B + group proteins type @atom:L + group proteins type @atom:N + } + + # LAMMPS has many available force field styles (and atom styles). + # Here, we pick the ones which work well for this molecular model: + + write_once("In Init") { + # --- Default options for the "1BeadFrustrated" protein model --- + # --- (These can be overridden later.) --- + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid table spline 360 + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + +} # 1beadFrustrated + + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt new file mode 100644 index 000000000..54e2de437 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt @@ -0,0 +1,85 @@ +import "1beadFrustrated.lt" + + +# Alternate starting conformation (same molecule): + + +1beadMisfolded inherits 1beadFrustrated { + + # This molecule "inherits" all of its features from "1beadFrustrated". + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876 + $atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251 + $atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085 + $atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451 + $atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135 + $atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977 + $atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409 + $atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275 + $atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938 + $atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398 + $atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186 + $atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916 + $atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704 + $atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331 + $atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056 + $atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167 + $atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633 + $atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523 + $atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791 + $atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346 + $atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555 + $atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946 + $atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493 + $atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934 + $atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086 + $atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181 + $atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868 + } + +} # 1beadMisfolded + + +1beadUnfolded inherits 1beadFrustrated { + + # This molecule "inherits" all of its features from "1beadFrustrated" + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 + $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 + $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 + $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 + $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 + $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 + $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 + $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 + $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 + $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 + $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 + $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 + $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 + $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 + $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 + $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 + $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 + $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 + $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 + $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 + $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 + $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 + $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 + $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 + $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 + $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 + $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 + } + +} # 1beadUnfolded + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py new file mode 100755 index 000000000..9b86809cc --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py @@ -0,0 +1,87 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between atoms in the +# protein and a chaperone provided in the supplemental materials section of: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# This is stored in a tabulated force field with a singularity at a distance R. +# +# To calculate the table for interaction between +# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181 +# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181 +# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True +# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True + +from math import * +import sys + +def U(r, eps, sigma, R, h): + #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h)) + # Formula is undefined at r=0, but you can take the limit: + if r <= 0: + return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0) + - h*pow((sigma/R), 6.0)) + xp = sigma/(r+R) + xm = sigma/(r-R) + term10 = pow(xm, 10.0) - pow(xp, 10.0) + term4 = pow(xm, 4.0) - pow(xp, 4.0) + return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4) + +def F(r, eps, sigma, R, h): + # Formula is undefined at r=0, but you can take the limit: + if r <= 0: + return 0.0 + product_term_a = U(r, eps, sigma, R, h) / r + ixp = (r+R)/sigma + ixm = (r-R)/sigma + dix_dr = 1.0/sigma + term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0)) + term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0)) + product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4) + return product_term_a + product_term_b + + +class InputError(Exception): + """ A generic exception object containing a string for error reporting. + + """ + def __init__(self, err_msg): + self.err_msg = err_msg + def __str__(self): + return self.err_msg + def __repr__(self): + return str(self) + +if len(sys.argv) < 8: + sys.stderr.write("Error: expected 7 arguments:\n" + "\n" + "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n") + sys.exit(-1) + +epsilon = float(sys.argv[1]) +sigma = float(sys.argv[2]) +R = float(sys.argv[3]) +h = float(sys.argv[4]) +rmin = float(sys.argv[5]) +rmax = float(sys.argv[6]) +N = int(sys.argv[7]) + +subtract_Urcut = False +if len(sys.argv) == 9: + subtract_Urcut = True +rcut = rmax + +for i in range(0,N): + r = rmin + i*(rmax-rmin)/(N-1) + U_r = U(r, epsilon, sigma, R, h) + F_r = F(r, epsilon, sigma, R, h) + if subtract_Urcut: + U_r -= U(rcut, epsilon, sigma, R, h) + if (r >= rcut) or (i==N-1): + U_r = 0.0 + F_r = 0.0 + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py new file mode 100755 index 000000000..34c66418a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py @@ -0,0 +1,67 @@ +#!/usr/bin/env python + +# Calculate a table of dihedral angle interactions used in the alpha-helix +# and beta-sheet regions of the frustrated protein model described in +# provided in figure 8 of the supplemental materials section of: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# Note that the "A" and "B" parameters were incorrectly reported to be +# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon. +# The phiA and phiB values were 57.29577951308232 degrees (1 rad) +# and 180 degrees, respectively. Both expA and expB were 6.0. +# +# To generate the table used for the alpha-helix (1 degree resolution) use this: +# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 +# To generate the table used for the beta-sheets (1 degree resolution) use this: +# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 +# +# (If you're curious as to why I set the location of the minima at phi_alpha +# to 1.0 radians (57.2957795 degrees), there was no particularly good reason. +# I think the correct value turns out to be something closer to 50 degrees.) + + +from math import * +import sys + + +# The previous version included the repulsive core term +def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False): + conv_units = pi/180.0 + if use_radians: + conv_units = 1.0 + termA = pow(cos(0.5*(phi-phiA)*conv_units), expA) + termB = pow(cos(0.5*(phi-phiB)*conv_units), expB) + return -A*termA - B*termB + +# The previous version included the repulsive core term +def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False): + conv_units = pi/180.0 + if use_radians: + conv_units = 1.0 + termA = (0.5*sin(0.5*(phi-phiA)*conv_units) * + expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0)) + termB = (0.5*sin(0.5*(phi-phiB)*conv_units) * + expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0)) + return -conv_units*(A*termA + B*termB) + +if len(sys.argv) != 10: + sys.stderr.write("Error: expected 9 arguments:\n" + "\n" + "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n") + sys.exit(-1) + +A = float(sys.argv[1]) +phiA = float(sys.argv[2]) +expA = float(sys.argv[3]) +B = float(sys.argv[4]) +phiB = float(sys.argv[5]) +expB = float(sys.argv[6]) +phi_min = float(sys.argv[7]) +phi_max = float(sys.argv[8]) +N = int(sys.argv[9]) + +for i in range(0,N): + phi = phi_min + i*(phi_max - phi_min)/(N-1) + U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False) + F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False) + print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt new file mode 100644 index 000000000..1d37823b7 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt @@ -0,0 +1,41 @@ +# Here we define a trivial molecule containing only one particle. + +Minichaperone { + + # atomID molID atomType charge x y z + + write("Data Atoms") { + $atom:C $mol @atom:C 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:C 100.0 + } + + write_once("In Settings") { + # If for some reason there are multiple chaperones present, + # I assume that they interact repulsively (hence, L=0) + + # i j pairStyle eps sig K L + + pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 3.0 1 0 + + # Optional: define the atoms in the "chaperonins" group: + # (Defining a group for the chaperone makes it easy to immobilize it later.) + + group chaperones type @atom:C + } + + # Specify which pair_styles, and atom styles work well with + # this model. (Again this can be overridden later.) + + write_once("In Init") { + units lj + atom_style full + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 8.0 9.0 + } + +} # Minichaperone + +# We have not specified how this particle interacts with other particles +# besides itself. Later on you must do this. diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt new file mode 100644 index 000000000..8f8c37d08 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt @@ -0,0 +1,72 @@ +write_once("Data Boundary") { + 0.0 80.0 xlo xhi + 0.0 80.0 ylo yhi + 0.0 80.0 zlo zhi +} + + +import "1beadFrustrated_variants.lt" +import "minichaperone.lt" + + +# Create 8 proteins and 8 chaperones (2x2x2 array): +# NOTE: Below I create multiple proteins and multiple chaperones +# to see what would happen. (I suspect nothing good. In the +# 2006 paper, only 1 protein and 1 chaperone were present.) + + +proteins = new 1beadUnfolded [2].move(40,0,0) + [2].move(0,40,0) + [2].move(0,0,40) + +chaperones = new Minichaperone [2].move(40,0,0) + [2].move(0,40,0) + [2].move(0,0,40) + +proteins[*][*][*].move(20,20,20) # to avoid overlap with the chaperones + + + +# If you only want 1 protein and 1 chaperone +# then replace the lines above with: +# +# protein = new 1beadMisfolded +# chaperone = new Minichaperone + + + + + +# ---- Now define interactions between the atoms in the protein ---- +# ---- (named "B", "L", "N") and the atom which represents the ---- +# ---- chaperone ("c"). These interactions are tabulated. ---- + +write_once("In Settings") { + pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/B table table_minichaperone_h=0.6.dat CH_H0.6 + pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/L table table_minichaperone_h=0.dat CH_H0 + pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/N table table_minichaperone_h=0.dat CH_H0 +} + +# Note: If you want purely repulsive spheres (crowding, h=0.0) +# instead of an attractive "hydrophobic" chaperone (h=0.6) +# then replace "table_minichaperone_h=0_6.dat CH_H0_6" +# with "table_minichaperone_h=0.dat CH_H0" +# (... or just use an ordinary Lennard-Jones interaction +# with sigma = 6.0 and epsilon near 0.0) + + +# LAMMPS has many available force field styles (and atom styles). Here we +# select the ones which work well for the full combine system. (This should +# override any settings made in "1beadFrustrated.lt" or "minichaperone.lt") + + +write_once("In Init") { + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid table spline 360 + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 981 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) +} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat new file mode 100644 index 000000000..d660fee30 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat @@ -0,0 +1,735 @@ +# Table of the potential and its negative derivative for frustrated alpha helix +# (Note: Derivatives are in units of energy/radians, not energy/degrees.) +# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 + +FRUSTRATED_ALPHA +N 360 DEGREES + +1 0.0 -2.74081145103 0.0783990792662 +2 1.0 -2.81950869101 0.0789852583442 +3 2.0 -2.89876136749 0.0795096391909 +4 3.0 -2.97850675562 0.0799703813963 +5 4.0 -3.05868032959 0.0803657243943 +6 5.0 -3.13921584545 0.0806939935737 +7 6.0 -3.22004543014 0.0809536062381 +8 7.0 -3.30109967628 0.0811430773977 +9 8.0 -3.38230774267 0.0812610253741 +10 9.0 -3.46359746038 0.0813061772009 +11 10.0 -3.54489544401 0.0812773738039 +12 11.0 -3.62612720812 0.0811735749433 +13 12.0 -3.70721728841 0.0809938639029 +14 13.0 -3.78808936748 0.080737451911 +15 14.0 -3.86866640485 0.0804036822781 +16 15.0 -3.94887077101 0.0799920342374 +17 16.0 -4.02862438516 0.0795021264757 +18 17.0 -4.10784885622 0.0789337203415 +19 18.0 -4.18646562704 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-1.85985831882 0.0672956071568 +350 349.0 -1.92773877092 0.0684595158069 +351 350.0 -1.99676540616 0.0695875914917 +352 351.0 -2.06690124527 0.0706775413231 +353 352.0 -2.13810701636 0.0717270740805 +354 353.0 -2.21034115987 0.0727339066469 +355 354.0 -2.28355983986 0.0736957705223 +356 355.0 -2.35771696194 0.0746104183955 +357 356.0 -2.43276419776 0.0754756307561 +358 357.0 -2.50865101613 0.0762892225281 +359 358.0 -2.58532472075 0.0770490497051 +360 359.0 -2.66273049463 0.0777530159679 + +# Table of the potential and its negative derivative for frustrated beta sheet +# (Note: Derivatives are in units of energy/radians, not energy/degrees.) +# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 + +FRUSTRATED_BETA +N 360 DEGREES + +1 0.0 -2.55809068762 0.0731724739818 +2 1.0 -2.63154144494 0.0737195744566 +3 2.0 -2.70551060968 0.0742089966437 +4 3.0 -2.77993963883 0.074639023134 +5 4.0 -2.85476830901 0.0750080115297 +6 5.0 -2.92993479441 0.0753144003899 +7 6.0 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a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat new file mode 100644 index 000000000..d2b1ed3aa --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat @@ -0,0 +1,988 @@ +# Interaction between a chaperone wall and hydrophobic ("B") beads (h=0.6) +# Generated using: +# generate_tables/calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True + +CH_H0.6 +N 981 R 3.1 8.0 + +1 3.1 24321971157.7 2.4400451019e+12 +2 3.105 14907528428.0 1.42456746092e+12 +3 3.11 9347010266.92 8.52735030437e+11 +4 3.115 5983057175.03 5.22187648991e+11 +5 3.12 3902942155.05 3.26496996649e+11 +6 3.125 2590648415.38 2.0808159227e+11 +7 3.13 1747350825.1 1.34970444886e+11 +8 3.135 1196139798.89 88984974583.5 +9 3.14 830130182.341 59559787515.6 +10 3.145 583518174.975 40428507749.3 +11 3.15 415078797.287 27803974550.9 +12 3.155 298562827.719 19356989964.4 +13 3.16 217001769.743 13631486848.5 +14 3.165 159270305.159 9703243449.66 +15 3.17 117976881.962 6977184032.49 +16 3.175 88149161.6455 5064988683.98 +17 3.18 66402860.1298 3710042118.5 +18 3.185 50409022.6215 2740737360.59 +19 3.19 38548170.6708 2041021063.98 +20 3.195 29683036.1074 1531572773.33 +21 3.2 23007502.8905 1157631256.92 +22 3.205 17945109.6836 881028781.898 +23 3.21 14080149.2893 674921399.554 +24 3.215 11110438.2418 520266326.167 +25 3.22 8814639.75879 403443800.764 +26 3.225 7029455.47123 314636408.027 +27 3.23 5633571.16439 246714657.082 +28 3.235 4536265.59262 194464091.949 +29 3.24 3669265.83647 154044868.616 +30 3.245 2980881.1453 122610915.077 +31 3.25 2431748.15466 98039536.8272 +32 3.255 1991724.07297 78738058.3506 +33 3.26 1637603.46485 63504600.2322 +34 3.265 1351429.90872 51427172.534 +35 3.27 1119240.11293 41810074.9071 +36 3.275 930124.378436 34119886.2947 +37 3.28 775519.857832 27945597.578 +38 3.285 648676.115123 22969017.4933 +39 3.29 544248.919174 18942684.9889 +40 3.295 457989.984944 15673297.5619 +41 3.3 386508.875651 13009215.1485 +42 3.305 327089.446276 10830991.226 +43 3.31 277547.709074 9044163.93118 +44 3.315 236121.303553 7573742.76366 +45 3.32 201383.18845 6359973.47163 +46 3.325 172173.978278 5355070.91875 +47 3.33 147548.691578 4520688.28477 +48 3.335 126734.684289 3825948.80978 +49 3.34 109098.298235 3245909.11014 +50 3.345 94118.3261235 2760354.93052 +51 3.35 81364.827777 2352853.97713 +52 3.355 70482.1624146 2010008.31682 +53 3.36 61175.3541703 1720862.26897 +54 3.365 53199.1018261 1476431.88582 +55 3.37 46348.8930587 1269329.84244 +56 3.375 40453.7990113 1093465.44786 +57 3.38 35370.6146686 943803.998782 +58 3.385 30979.0803706 816173.162054 +59 3.39 27177.9744013 707106.743488 +60 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-3.09346599767e-05 -0.00207982254527 +979 7.99 -2.05648617073e-05 -0.00206810960966 +980 7.995 -1.0253435891e-05 -0.00205647346771 +981 8.0 0.0 0.0 diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat new file mode 100644 index 000000000..82eaa7e15 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat @@ -0,0 +1,989 @@ +# Interaction between a chaperone wall and hydrophilic ("L", "N") beads (h=0.0) +# Generated using: +# generate_tables/calc_chaperone_table.py 1.0 1.0 3.0 0.00 3.1 8.0 981 True + +CH_H0 +N 981 R 3.1 8.0 + +1 3.1 24322007640.7 2.44004657299e+12 +2 3.105 14907558394.3 1.42456861215e+12 +3 3.11 9347035105.18 8.52735941633e+11 +4 3.115 5983077933.86 5.22188377701e+11 +5 3.12 3902959636.31 3.26497584961e+11 +6 3.125 2590663239.27 2.08082071378e+11 +7 3.13 1747363476.38 1.34970838198e+11 +8 3.135 1196150660.14 88985299862.7 +9 3.14 830139558.184 59560058382.9 +10 3.145 583526310.01 40428734750.9 +11 3.15 415085889.414 27804165925.8 +12 3.155 298569038.21 19357152203.7 +13 3.16 217007230.904 13631625105.8 +14 3.165 159275126.218 9703361847.17 +15 3.17 117981153.625 6977285889.84 +16 3.175 88152959.6539 5065076691.93 +17 3.18 66406248.0614 3710118471.36 +18 3.185 50412054.1061 2740803858.1 +19 3.19 38550891.1571 2041079190.29 +20 3.195 29685484.2812 1531623758.63 +21 3.2 23009711.8183 1157676125.86 +22 3.205 17947107.7408 881068391.885 +23 3.21 14081960.9175 674956471.214 +24 3.215 11112084.5698 520297467.685 +25 3.22 8816139.11379 403471527.483 +26 3.225 7030823.80219 314661158.279 +27 3.23 5634822.39381 246736805.049 +28 3.235 4537411.91017 194483958.161 +29 3.24 3670317.94503 154062728.557 +30 3.245 2981848.4679 122627006.268 +31 3.25 2432639.00923 98054064.6797 +32 3.255 1992545.82032 78751201.0309 +33 3.26 1638362.63452 63516512.707 +34 3.265 1352132.30623 51437989.9558 +35 3.27 1119890.91156 41819915.4536 +36 3.275 930728.197936 34128853.5593 +37 3.28 776080.832192 27953782.5881 +38 3.285 649197.950984 22976500.4202 +39 3.29 544734.946388 18949536.6006 +40 3.295 458443.200409 15679580.461 +41 3.3 386931.981432 13014984.83 +42 3.305 327484.882814 10836296.983 +43 3.31 277917.684205 9049049.63384 +44 3.315 236467.817902 7578247.52911 +45 3.32 201708.057716 6364132.2427 +46 3.325 172478.852825 5358914.96458 +47 3.33 147835.073691 4524245.63494 +48 3.335 127003.943407 3829244.63171 +49 3.34 109351.684422 3248966.03768 +50 3.345 94356.982001 2763193.35086 +51 3.35 81589.7991199 2355492.28163 +52 3.355 70694.4075656 2012463.12085 +53 3.36 61375.7524283 1723148.60489 +54 3.365 53388.4609277 1478563.37272 +55 3.37 46527.9558627 1271318.83571 +56 3.375 40623.2494805 1095323.17118 +57 3.38 35531.0832305 945540.660872 +58 3.385 31131.1487289 817798.059995 +59 3.39 27322.1798598 708628.354433 +60 3.395 24018.7487675 615144.330958 +61 3.4 21148.6321858 534935.990585 +62 3.405 18650.6411473 465987.08561 +63 3.41 16472.8281676 406607.038172 +64 3.415 14571.00272 355375.264352 +65 3.42 12907.4991276 311095.530355 +66 3.425 11450.1516342 272758.442538 +67 3.43 10171.439929 239510.549012 +68 3.435 9047.7752383 210628.82877 +69 3.44 8058.90260095 185499.581541 +70 3.445 7187.39938846 163600.920836 +71 3.45 6418.25372556 144488.223969 +72 3.455 5738.50938334 127782.014261 +73 3.46 5136.9660889 113157.848128 +74 3.465 4603.92612777 100337.85845 +75 3.47 4130.97969454 89083.6690543 +76 3.475 3710.8227393 79190.4466465 +77 3.48 3337.10211855 70481.8981958 +78 3.485 3004.28373073 62806.0557792 +79 3.49 2707.54003568 56031.718535 +80 3.495 2442.65394998 50045.4440029 +81 3.5 2205.93660145 44748.9996316 +82 3.505 1994.15683268 40057.2004294 +83 3.51 1804.48068152 35896.0712099 +84 3.515 1634.41934741 32201.2821773 +85 3.52 1481.78438725 28916.8150767 +86 3.525 1344.64907977 25993.8241582 +87 3.53 1221.31506159 23389.6620133 +88 3.535 1110.28347503 21067.0451721 +89 3.54 1010.22998333 18993.3383579 +90 3.545 919.9831055 17139.9396418 +91 3.55 838.505404885 15481.7515237 +92 3.555 764.877134293 13996.7253013 +93 3.56 698.281998657 12665.4680354 +94 3.565 637.994745566 11470.9030593 +95 3.57 583.370335637 10397.9763514 +96 3.575 533.834480178 9433.40224818 +97 3.58 488.875363677 8565.44294671 +98 3.585 448.036394307 7783.71706925 +99 3.59 410.909847488 7079.03325566 +100 3.595 377.131286207 6443.24533767 +101 3.6 346.374657747 5869.126147 +102 3.605 318.34798013 5350.25743201 +103 3.61 292.789543287 4880.93371692 +104 3.615 269.464560006 4456.07824337 +105 3.62 248.162210353 4071.16939457 +106 3.625 228.693030668 3722.17622503 +107 3.63 210.886604667 3405.5019084 +108 3.635 194.589519671 3117.93407879 +109 3.64 179.663555764 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2.56155599635e-07 +963 7.91 2.05362531363e-08 2.53146154374e-07 +964 7.915 1.92779660724e-08 2.50175010842e-07 +965 7.92 1.8034440067e-08 2.47241644098e-07 +966 7.925 1.68054875325e-08 2.44345536912e-07 +967 7.93 1.55909234484e-08 2.41486179638e-07 +968 7.935 1.43905653237e-08 2.38663070101e-07 +969 7.94 1.32042331597e-08 2.35875713474e-07 +970 7.945 1.20317494138e-08 2.33123622171e-07 +971 7.95 1.08729389636e-08 2.30406315726e-07 +972 7.955 9.72762907123e-09 2.27723320689e-07 +973 7.96 8.59564934896e-09 2.2507417051e-07 +974 7.965 7.47683172465e-09 2.2245840544e-07 +975 7.97 6.37101040818e-09 2.19875572416e-07 +976 7.975 5.27802185823e-09 2.17325224966e-07 +977 7.98 4.19770474957e-09 2.148069231e-07 +978 7.985 3.12989994095e-09 2.12320233213e-07 +979 7.99 2.07445044336e-09 2.09864727985e-07 +980 7.995 1.03120138888e-09 2.07439986287e-07 +981 8.0 0.0 0.0 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min new file mode 100644 index 000000000..e2d4a5cce --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min @@ -0,0 +1,24 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# Optional: Make sure the pairwise energies look reasonable: +pair_write 1 4 1001 r 4.05 8 test_chap-B.dat C-B 0 0 +pair_write 2 4 1001 r 4.05 8 test_chap-L.dat C-L 0 0 +pair_write 3 4 1001 r 4.05 8 test_chap-N.dat C-N 0 0 + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt new file mode 100644 index 000000000..523a16575 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt @@ -0,0 +1,46 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.025 +dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +fix fxlan all langevin 0.25 0.25 1.0 48279 +fix fxnve all nve + +# Notes: +# The temperature is in reduced units and is set to 0.25 +# which is the folding temperature for the frustrated protein +# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, +# as it was in the paper. (Hopefully folding times should be similar.) +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 5000 #(time interval for printing out "thermo" data) + +#restart 100000000 restart_nvt + +run 1000000000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README.TXT new file mode 100644 index 000000000..77af3de15 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README.TXT @@ -0,0 +1,29 @@ +# This directory demonstrates how to run a short simulation of +# the "frustrated" coarse-grained protein model used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) +# +# During this short simulation (run_short_sim.nvt.in) the protein evolves +# from an unfolded initial conformation to a misfolded conformation. +# (Visualize using VMD. Note: It can take hundreds of millions of +# timesteps to escape from this conformation and reach the folded state.) +# +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh new file mode 100755 index 000000000..99338c770 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh @@ -0,0 +1,21 @@ +# You would probably run lammps this way: +# +# lmp_ubuntu -i run.in.nvt + +# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer +# to the input scripts & data files you created earlier when you ran moltemplate +# system.in.init, system.in.settings, system.data + + +# ----------------------------------- + +LAMMPS_COMMAND="lmp_ubuntu" + +# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. + +# Run lammps using the following 3 commands: + +"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +"$LAMMPS_COMMAND" -i run_short_sim.in.nvt # production run + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh new file mode 100755 index 000000000..f2462426f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh @@ -0,0 +1,24 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -overlay-dihdedrals system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + cp -r table*.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt new file mode 100644 index 000000000..019afc144 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 000000000..c7f8572b2 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,85 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 27 !NATOM + 1 1 2 2 0.000000 1.0000 0 + 2 1 1 1 0.000000 1.0000 0 + 3 1 2 2 0.000000 1.0000 0 + 4 1 1 1 0.000000 1.0000 0 + 5 1 2 2 0.000000 1.0000 0 + 6 1 1 1 0.000000 1.0000 0 + 7 1 3 3 0.000000 1.0000 0 + 8 1 3 3 0.000000 1.0000 0 + 9 1 1 1 0.000000 1.0000 0 + 10 1 2 2 0.000000 1.0000 0 + 11 1 1 1 0.000000 1.0000 0 + 12 1 2 2 0.000000 1.0000 0 + 13 1 1 1 0.000000 1.0000 0 + 14 1 2 2 0.000000 1.0000 0 + 15 1 3 3 0.000000 1.0000 0 + 16 1 3 3 0.000000 1.0000 0 + 17 1 3 3 0.000000 1.0000 0 + 18 1 1 1 0.000000 1.0000 0 + 19 1 1 1 0.000000 1.0000 0 + 20 1 2 2 0.000000 1.0000 0 + 21 1 2 2 0.000000 1.0000 0 + 22 1 1 1 0.000000 1.0000 0 + 23 1 1 1 0.000000 1.0000 0 + 24 1 2 2 0.000000 1.0000 0 + 25 1 2 2 0.000000 1.0000 0 + 26 1 1 1 0.000000 1.0000 0 + 27 1 2 2 0.000000 1.0000 0 + + 26 !NBOND: bonds + 1 2 2 3 3 4 4 5 + 5 6 6 7 7 8 8 9 + 9 10 10 11 11 12 12 13 + 13 14 14 15 15 16 16 17 + 17 18 18 19 19 20 20 21 + 21 22 22 23 23 24 24 25 + 25 26 26 27 + + 25 !NTHETA: angles + 13 14 15 7 8 9 6 7 8 + 16 17 18 15 16 17 2 3 4 + 4 5 6 9 10 11 11 12 13 + 14 15 16 1 2 3 3 4 5 + 10 11 12 12 13 14 25 26 27 + 5 6 7 8 9 10 17 18 19 + 18 19 20 22 23 24 21 22 23 + 19 20 21 20 21 22 23 24 25 + 24 25 26 + + 19 !NPHI: dihedrals + 1 2 3 4 2 3 4 5 + 3 4 5 6 4 5 6 7 + 8 9 10 11 9 10 11 12 + 10 11 12 13 11 12 13 14 + 12 13 14 15 15 16 17 18 + 16 17 18 19 17 18 19 20 + 18 19 20 21 19 20 21 22 + 20 21 22 23 21 22 23 24 + 22 23 24 25 23 24 25 26 + 24 25 26 27 + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg new file mode 100644 index 000000000..0869126bd Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg new file mode 100644 index 000000000..357bc780a Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt new file mode 100644 index 000000000..074b55c73 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt @@ -0,0 +1,216 @@ +# This file defines the "frustrated" coarse-grained protein model used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) + + +1beadFrustrated { + + # There are 3 atom types (referred to above as B, L, and N) + # Define their masses: + + write_once("Data Masses") { + @atom:B 1.0 + @atom:L 1.0 + @atom:N 1.0 + } + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679 + $atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341 + $atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966 + $atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709 + $atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737 + $atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098 + $atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919 + $atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901 + $atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617 + $atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043 + $atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721 + $atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951 + $atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019 + $atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217 + $atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429 + $atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711 + $atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358 + $atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719 + $atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014 + $atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053 + $atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748 + $atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224 + $atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255 + $atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346 + $atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166 + $atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097 + $atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463 + } + + # bond-ID bond-Type atom-ID atom-ID + + write("Data Bonds") { + $bond:b1 @bond:backbone $atom:a1 $atom:a2 + $bond:b2 @bond:backbone $atom:a2 $atom:a3 + $bond:b3 @bond:backbone $atom:a3 $atom:a4 + $bond:b4 @bond:backbone $atom:a4 $atom:a5 + $bond:b5 @bond:backbone $atom:a5 $atom:a6 + $bond:b6 @bond:backbone $atom:a6 $atom:a7 + $bond:b7 @bond:backbone $atom:a7 $atom:a8 + $bond:b8 @bond:backbone $atom:a8 $atom:a9 + $bond:b9 @bond:backbone $atom:a9 $atom:a10 + $bond:b10 @bond:backbone $atom:a10 $atom:a11 + $bond:b11 @bond:backbone $atom:a11 $atom:a12 + $bond:b12 @bond:backbone $atom:a12 $atom:a13 + $bond:b13 @bond:backbone $atom:a13 $atom:a14 + $bond:b14 @bond:backbone $atom:a14 $atom:a15 + $bond:b15 @bond:backbone $atom:a15 $atom:a16 + $bond:b16 @bond:backbone $atom:a16 $atom:a17 + $bond:b17 @bond:backbone $atom:a17 $atom:a18 + $bond:b18 @bond:backbone $atom:a18 $atom:a19 + $bond:b19 @bond:backbone $atom:a19 $atom:a20 + $bond:b20 @bond:backbone $atom:a20 $atom:a21 + $bond:b21 @bond:backbone $atom:a21 $atom:a22 + $bond:b22 @bond:backbone $atom:a22 $atom:a23 + $bond:b23 @bond:backbone $atom:a23 $atom:a24 + $bond:b24 @bond:backbone $atom:a24 $atom:a25 + $bond:b25 @bond:backbone $atom:a25 $atom:a26 + $bond:b26 @bond:backbone $atom:a26 $atom:a27 + } + + # (3-body) Angles are specified below + + # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. + # (These interactions are not determined by atom type.) + + # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID + + write("Data Dihedrals") { + + $dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7 + + # Dihedral angle forces in the turn regions were switched off + # (in this model) so just I comment them out (and \ the variable names). + # \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8 + # \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9 + # \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10 + + $dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15 + + # Dihedral angle forces in the turn regions were switched off + # (in this model) so just I comment them out (and \ the variable names). + # \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16 + # \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17 + + $dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27 + } + + # All consecutively bonded triplets of atoms same 3-body bond-angle + # interaction parameters. Of coarse, we could specify them all explicitly + # (as we did for the dihedrals above), but I wanted to show how to specify + # angles by atom type instead. (You can do this for dihedrals & impropers + # also.) + + # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type + + write_once("Data Angles By Type") { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # (The "*" is a wildcard character. I use "*" to denote any atom-type or + # bond-type which is defined within the current namespace: 1beadFrustrated) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 + pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 + pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 + } + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond-Type bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 100.0 1.0 + } + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # angle-Type anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 13.3333333333 105.0 + } + + + # We use tabular dihedral potentials to implement the dihedral forces. + # (Actually there is a way to use Fourier series, using multiple charmm + # style dihedral interactions, but it's slower and messier.) + + write_once("In Settings") { + # style file keyword + dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA + dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA + # No need to specify dihedral interactions in the turn regions. (none exist) + } + + write_once("In Settings") { + # Optional: define the atoms in the "proteins" group + group proteins type @atom:B + group proteins type @atom:L + group proteins type @atom:N + } + + # LAMMPS has many available force field styles (and atom styles). + # Here, we pick the ones which work well for this molecular model: + + write_once("In Init") { + # --- Default options for the "1BeadFrustrated" protein model --- + # --- (These can be overridden later.) --- + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid table spline 360 + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + +} # 1beadFrustrated + + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt new file mode 100644 index 000000000..54e2de437 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt @@ -0,0 +1,85 @@ +import "1beadFrustrated.lt" + + +# Alternate starting conformation (same molecule): + + +1beadMisfolded inherits 1beadFrustrated { + + # This molecule "inherits" all of its features from "1beadFrustrated". + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876 + $atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251 + $atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085 + $atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451 + $atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135 + $atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977 + $atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409 + $atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275 + $atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938 + $atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398 + $atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186 + $atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916 + $atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704 + $atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331 + $atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056 + $atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167 + $atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633 + $atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523 + $atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791 + $atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346 + $atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555 + $atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946 + $atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493 + $atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934 + $atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086 + $atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181 + $atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868 + } + +} # 1beadMisfolded + + +1beadUnfolded inherits 1beadFrustrated { + + # This molecule "inherits" all of its features from "1beadFrustrated" + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 + $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 + $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 + $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 + $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 + $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 + $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 + $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 + $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 + $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 + $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 + $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 + $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 + $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 + $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 + $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 + $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 + $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 + $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 + $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 + $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 + $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 + $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 + $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 + $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 + $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 + $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 + } + +} # 1beadUnfolded + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py new file mode 100755 index 000000000..34c66418a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py @@ -0,0 +1,67 @@ +#!/usr/bin/env python + +# Calculate a table of dihedral angle interactions used in the alpha-helix +# and beta-sheet regions of the frustrated protein model described in +# provided in figure 8 of the supplemental materials section of: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# Note that the "A" and "B" parameters were incorrectly reported to be +# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon. +# The phiA and phiB values were 57.29577951308232 degrees (1 rad) +# and 180 degrees, respectively. Both expA and expB were 6.0. +# +# To generate the table used for the alpha-helix (1 degree resolution) use this: +# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 +# To generate the table used for the beta-sheets (1 degree resolution) use this: +# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 +# +# (If you're curious as to why I set the location of the minima at phi_alpha +# to 1.0 radians (57.2957795 degrees), there was no particularly good reason. +# I think the correct value turns out to be something closer to 50 degrees.) + + +from math import * +import sys + + +# The previous version included the repulsive core term +def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False): + conv_units = pi/180.0 + if use_radians: + conv_units = 1.0 + termA = pow(cos(0.5*(phi-phiA)*conv_units), expA) + termB = pow(cos(0.5*(phi-phiB)*conv_units), expB) + return -A*termA - B*termB + +# The previous version included the repulsive core term +def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False): + conv_units = pi/180.0 + if use_radians: + conv_units = 1.0 + termA = (0.5*sin(0.5*(phi-phiA)*conv_units) * + expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0)) + termB = (0.5*sin(0.5*(phi-phiB)*conv_units) * + expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0)) + return -conv_units*(A*termA + B*termB) + +if len(sys.argv) != 10: + sys.stderr.write("Error: expected 9 arguments:\n" + "\n" + "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n") + sys.exit(-1) + +A = float(sys.argv[1]) +phiA = float(sys.argv[2]) +expA = float(sys.argv[3]) +B = float(sys.argv[4]) +phiB = float(sys.argv[5]) +expB = float(sys.argv[6]) +phi_min = float(sys.argv[7]) +phi_max = float(sys.argv[8]) +N = int(sys.argv[9]) + +for i in range(0,N): + phi = phi_min + i*(phi_max - phi_min)/(N-1) + U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False) + F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False) + print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt new file mode 100644 index 000000000..a27595559 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt @@ -0,0 +1,20 @@ +import "1beadFrustrated_variants.lt" + + +protein = new 1beadUnfolded + + + +# Note: The protein begins in an "Unfolded" conformation. If instead +# you want it to begin in the folded or misfolded conformations use: +# protein = new 1beadFrustrated # or +# protein = new 1beadMisfolded + + + +# ("27.0" is the length of the protein when maximally extended) +write_once("Data Boundary") { + 0.0 27.0 xlo xhi + 0.0 27.0 ylo yhi + 0.0 27.0 zlo zhi +} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat new file mode 100644 index 000000000..d660fee30 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat @@ -0,0 +1,735 @@ +# Table of the potential and its negative derivative for frustrated alpha helix +# (Note: Derivatives are in units of energy/radians, not energy/degrees.) +# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 + +FRUSTRATED_ALPHA +N 360 DEGREES + +1 0.0 -2.74081145103 0.0783990792662 +2 1.0 -2.81950869101 0.0789852583442 +3 2.0 -2.89876136749 0.0795096391909 +4 3.0 -2.97850675562 0.0799703813963 +5 4.0 -3.05868032959 0.0803657243943 +6 5.0 -3.13921584545 0.0806939935737 +7 6.0 -3.22004543014 0.0809536062381 +8 7.0 -3.30109967628 0.0811430773977 +9 8.0 -3.38230774267 0.0812610253741 +10 9.0 -3.46359746038 0.0813061772009 +11 10.0 -3.54489544401 0.0812773738039 +12 11.0 -3.62612720812 0.0811735749433 +13 12.0 -3.70721728841 0.0809938639029 +14 13.0 -3.78808936748 0.080737451911 +15 14.0 -3.86866640485 0.0804036822781 +16 15.0 -3.94887077101 0.0799920342374 +17 16.0 -4.02862438516 0.0795021264757 +18 17.0 -4.10784885622 0.0789337203415 +19 18.0 -4.18646562704 0.0782867227197 +20 19.0 -4.26439612115 0.0775611885609 +21 20.0 -4.34156189202 0.0767573230567 +22 21.0 -4.41788477419 0.0758754834523 +23 22.0 -4.49328703609 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0.0706775413231 +353 352.0 -2.13810701636 0.0717270740805 +354 353.0 -2.21034115987 0.0727339066469 +355 354.0 -2.28355983986 0.0736957705223 +356 355.0 -2.35771696194 0.0746104183955 +357 356.0 -2.43276419776 0.0754756307561 +358 357.0 -2.50865101613 0.0762892225281 +359 358.0 -2.58532472075 0.0770490497051 +360 359.0 -2.66273049463 0.0777530159679 + +# Table of the potential and its negative derivative for frustrated beta sheet +# (Note: Derivatives are in units of energy/radians, not energy/degrees.) +# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 + +FRUSTRATED_BETA +N 360 DEGREES + +1 0.0 -2.55809068762 0.0731724739818 +2 1.0 -2.63154144494 0.0737195744566 +3 2.0 -2.70551060968 0.0742089966437 +4 3.0 -2.77993963883 0.074639023134 +5 4.0 -2.85476830901 0.0750080115297 +6 5.0 -2.92993479441 0.0753144003899 +7 6.0 -3.00537575069 0.0755567150326 +8 7.0 -3.08102640456 0.0757335731758 +9 8.0 -3.15682064892 0.0758436903983 +10 9.0 -3.23269114341 0.075885885404 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b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run.in.min new file mode 100644 index 000000000..fce9843aa --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run.in.min @@ -0,0 +1,19 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt new file mode 100644 index 000000000..2974c12e8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt @@ -0,0 +1,50 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.025 +dump 1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +# Keep the chaperonin fixed. Only let the protein move. + +fix fxlan proteins langevin 0.25 0.25 1.0 48279 +fix fxnve proteins nve + +# Notes: +# The temperature is in reduced units and is set to 0.25 +# which is the folding temperature for the frustrated protein +# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, +# as it was in the paper. (Hopefully folding times should be similar.) +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 50 #(time interval for printing out "thermo" data) + +#restart 100000000 restart_nvt + +# Just run it long enough for it to collapse (not fold) +# (If you need to run it longer, then dump trajectory data less frequently.) +run 50000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT new file mode 100644 index 000000000..5da41b9a8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT @@ -0,0 +1,32 @@ +# This directory demonstrates how to run a short simulation of +# the "unfrustrated" coarse-grained protein model used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) +# +# In this example, the protein is placed inside a repulsive sphere +# of radius 6.0 sigma which confines its motion. +# (This sphere is sometimes called the "chaperonin", because +# we were using it to model the crude behavior of a chaperonin cavity.) +# +# During this short simulation (run.in.nvt) the protein evolves +# from an unfolded initial conformation to the folded state. +# +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh new file mode 100755 index 000000000..45bd2d451 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh @@ -0,0 +1,31 @@ +# You would probably run lammps this way: +# +# lmp_ubuntu -i run.in.nvt + +# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer +# to the input scripts & data files you created earlier when you ran moltemplate +# system.in.init, system.in.settings, system.data + + + + +# ----------------------------------- + + + +LAMMPS_COMMAND="lmp_ubuntu" + +# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. + +# Run lammps using the following 3 commands: + +"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +"$LAMMPS_COMMAND" -i run.in.nvt # production run + +# Alternately, if you have MPI installed, try something like this: + +#NUMPROCS=4 +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh new file mode 100755 index 000000000..f2462426f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh @@ -0,0 +1,24 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -overlay-dihdedrals system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + cp -r table*.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt new file mode 100644 index 000000000..019afc144 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 000000000..7763505c0 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,98 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 28 !NATOM + 1 1 1 1 0.000000 100.0000 0 + 2 2 3 3 0.000000 1.0000 0 + 3 2 2 2 0.000000 1.0000 0 + 4 2 3 3 0.000000 1.0000 0 + 5 2 2 2 0.000000 1.0000 0 + 6 2 3 3 0.000000 1.0000 0 + 7 2 2 2 0.000000 1.0000 0 + 8 2 4 4 0.000000 1.0000 0 + 9 2 4 4 0.000000 1.0000 0 + 10 2 2 2 0.000000 1.0000 0 + 11 2 3 3 0.000000 1.0000 0 + 12 2 2 2 0.000000 1.0000 0 + 13 2 3 3 0.000000 1.0000 0 + 14 2 2 2 0.000000 1.0000 0 + 15 2 3 3 0.000000 1.0000 0 + 16 2 4 4 0.000000 1.0000 0 + 17 2 4 4 0.000000 1.0000 0 + 18 2 4 4 0.000000 1.0000 0 + 19 2 2 2 0.000000 1.0000 0 + 20 2 2 2 0.000000 1.0000 0 + 21 2 3 3 0.000000 1.0000 0 + 22 2 3 3 0.000000 1.0000 0 + 23 2 2 2 0.000000 1.0000 0 + 24 2 2 2 0.000000 1.0000 0 + 25 2 3 3 0.000000 1.0000 0 + 26 2 3 3 0.000000 1.0000 0 + 27 2 2 2 0.000000 1.0000 0 + 28 2 3 3 0.000000 1.0000 0 + + 26 !NBOND: bonds + 2 3 3 4 4 5 5 6 + 6 7 7 8 8 9 9 10 + 10 11 11 12 12 13 13 14 + 14 15 15 16 16 17 17 18 + 18 19 19 20 20 21 21 22 + 22 23 23 24 24 25 25 26 + 26 27 27 28 + + 25 !NTHETA: angles + 3 4 5 5 6 7 10 11 12 + 12 13 14 8 9 10 7 8 9 + 17 18 19 19 20 21 23 24 25 + 22 23 24 2 3 4 4 5 6 + 11 12 13 13 14 15 26 27 28 + 15 16 17 6 7 8 9 10 11 + 14 15 16 18 19 20 20 21 22 + 21 22 23 24 25 26 25 26 27 + 16 17 18 + + 43 !NPHI: dihedrals + 2 3 4 5 2 3 4 5 + 3 4 5 6 3 4 5 6 + 4 5 6 7 4 5 6 7 + 5 6 7 8 5 6 7 8 + 6 7 8 9 7 8 9 10 + 8 9 10 11 9 10 11 12 + 9 10 11 12 10 11 12 13 + 10 11 12 13 11 12 13 14 + 11 12 13 14 12 13 14 15 + 12 13 14 15 13 14 15 16 + 13 14 15 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b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt new file mode 100644 index 000000000..0dc1f5dd0 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt @@ -0,0 +1,255 @@ +# This file defines a pair of coarse-grained protein models used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) + + +1beadUnfrustrated { + + # Note: the "unfrustrated" model is kind of funny looking. (My apologies.) + + # There are 3 atom types (referred to above as B, L, and N) + # Define their masses: + + write_once("Data Masses") { + @atom:B 1.0 + @atom:L 1.0 + @atom:N 1.0 + } + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -1.3969548 1.7525716 -0.28565118 + $atom:a2 $mol @atom:B 0.0 -0.66847917 1.0738923 -0.39651074 + $atom:a3 $mol @atom:L 0.0 -0.16610379 1.0893417 0.44519456 + $atom:a4 $mol @atom:B 0.0 0.42244126 0.35006314 0.15979926 + $atom:a5 $mol @atom:L 0.0 1.2844393 0.55103218 0.64505356 + $atom:a6 $mol @atom:N 0.0 1.9703715 0.37775946 -0.05267634 + $atom:a7 $mol @atom:N 0.0 2.574926 -0.30399114 0.34330503 + $atom:a8 $mol @atom:N 0.0 2.029546 -1.1256647 0.19829852 + $atom:a9 $mol @atom:B 0.0 1.0936146 -0.76054936 0.1043528 + $atom:a10 $mol @atom:L 0.0 0.74888247 -0.81165991 1.0334863 + $atom:a11 $mol @atom:B 0.0 -0.069536333 -0.26815389 0.94356636 + $atom:a12 $mol @atom:L 0.0 -0.65671052 -0.522532 1.7113065 + $atom:a13 $mol @atom:N 0.0 -1.5278507 -0.10774689 1.4611921 + $atom:a14 $mol @atom:L 0.0 -2.1958878 -0.8403146 1.5521738 + $atom:a15 $mol @atom:N 0.0 -2.6058074 -0.86553455 0.64397232 + $atom:a16 $mol @atom:N 0.0 -1.8447588 -1.1286421 0.042924693 + $atom:a17 $mol @atom:N 0.0 -1.5328721 -0.28576244 -0.40564841 + $atom:a18 $mol @atom:B 0.0 -0.69593879 0.027664412 0.064884008 + $atom:a19 $mol @atom:B 0.0 0.0026517494 -0.66355162 -0.11470678 + $atom:a20 $mol @atom:L 0.0 -0.35479285 -1.2282381 -0.86455878 + $atom:a21 $mol @atom:L 0.0 -0.60202976 -0.47829758 -1.4411001 + $atom:a22 $mol @atom:B 0.0 -0.14616501 0.20157397 -0.87098365 + $atom:a23 $mol @atom:B 0.0 0.7755198 -0.14153019 -0.76838748 + $atom:a24 $mol @atom:L 0.0 1.2465693 0.19738595 -1.5794731 + $atom:a25 $mol @atom:L 0.0 0.77604792 1.0612244 -1.637442 + $atom:a26 $mol @atom:B 0.0 0.44801303 1.1110219 -0.6900789 + $atom:a27 $mol @atom:L 0.0 1.0908651 1.7386382 -0.24229241 + } + + # bond-ID bond-Type atom-ID atom-ID + + write("Data Bonds") { + $bond:b1 @bond:backbone $atom:a1 $atom:a2 + $bond:b2 @bond:backbone $atom:a2 $atom:a3 + $bond:b3 @bond:backbone $atom:a3 $atom:a4 + $bond:b4 @bond:backbone $atom:a4 $atom:a5 + $bond:b5 @bond:backbone $atom:a5 $atom:a6 + $bond:b6 @bond:backbone $atom:a6 $atom:a7 + $bond:b7 @bond:backbone $atom:a7 $atom:a8 + $bond:b8 @bond:backbone $atom:a8 $atom:a9 + $bond:b9 @bond:backbone $atom:a9 $atom:a10 + $bond:b10 @bond:backbone $atom:a10 $atom:a11 + $bond:b11 @bond:backbone $atom:a11 $atom:a12 + $bond:b12 @bond:backbone $atom:a12 $atom:a13 + $bond:b13 @bond:backbone $atom:a13 $atom:a14 + $bond:b14 @bond:backbone $atom:a14 $atom:a15 + $bond:b15 @bond:backbone $atom:a15 $atom:a16 + $bond:b16 @bond:backbone $atom:a16 $atom:a17 + $bond:b17 @bond:backbone $atom:a17 $atom:a18 + $bond:b18 @bond:backbone $atom:a18 $atom:a19 + $bond:b19 @bond:backbone $atom:a19 $atom:a20 + $bond:b20 @bond:backbone $atom:a20 $atom:a21 + $bond:b21 @bond:backbone $atom:a21 $atom:a22 + $bond:b22 @bond:backbone $atom:a22 $atom:a23 + $bond:b23 @bond:backbone $atom:a23 $atom:a24 + $bond:b24 @bond:backbone $atom:a24 $atom:a25 + $bond:b25 @bond:backbone $atom:a25 $atom:a26 + $bond:b26 @bond:backbone $atom:a26 $atom:a27 + } + + # (3-body) Angles are specified below + + # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. + # (These interactions are not determined by atom type.) + # + # Note that some quartets of atoms are listed because their + # potentials contain multiple terms in the Fourier expansion. + # (IE. multiple cosines... Be sure to use "-overlay-dihedrals"!) + # + # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID + + write("Data Dihedrals") { + $dihedral:d1a @dihedral:beta1 $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d1b @dihedral:beta2 $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d2a @dihedral:beta1 $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d2b @dihedral:beta2 $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d3a @dihedral:beta1 $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d3b @dihedral:beta2 $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d4a @dihedral:beta1 $atom:a4 $atom:a5 $atom:a6 $atom:a7 + $dihedral:d4b @dihedral:beta2 $atom:a4 $atom:a5 $atom:a6 $atom:a7 + $dihedral:d5 @dihedral:turn1 $atom:a5 $atom:a6 $atom:a7 $atom:a8 + $dihedral:d6 @dihedral:turn2 $atom:a6 $atom:a7 $atom:a8 $atom:a9 + $dihedral:d7 @dihedral:turn3 $atom:a7 $atom:a8 $atom:a9 $atom:a10 + $dihedral:d8a @dihedral:beta1 $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d8b @dihedral:beta2 $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d9a @dihedral:beta1 $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d9b @dihedral:beta2 $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d10a @dihedral:beta1 $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d10b @dihedral:beta2 $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d11a @dihedral:beta1 $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d11b @dihedral:beta2 $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d12a @dihedral:beta1 $atom:a12 $atom:a13 $atom:a14 $atom:a15 + $dihedral:d12b @dihedral:beta2 $atom:a12 $atom:a13 $atom:a14 $atom:a15 + $dihedral:d13 @dihedral:turn4 $atom:a13 $atom:a14 $atom:a15 $atom:a16 + $dihedral:d14 @dihedral:turn5 $atom:a14 $atom:a15 $atom:a16 $atom:a17 + $dihedral:d15a @dihedral:alpha1 $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d15b @dihedral:alpha2 $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d16a @dihedral:alpha1 $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d16b @dihedral:alpha2 $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d17a @dihedral:alpha1 $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d17b @dihedral:alpha2 $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d18a @dihedral:alpha1 $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d18b @dihedral:alpha2 $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d19a @dihedral:alpha1 $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d19b @dihedral:alpha2 $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d20a @dihedral:alpha1 $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d20b @dihedral:alpha2 $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d21a @dihedral:alpha1 $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d21b @dihedral:alpha2 $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d22a @dihedral:alpha1 $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d22b @dihedral:alpha2 $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d23a @dihedral:alpha1 $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d23b @dihedral:alpha2 $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d24a @dihedral:alpha1 $atom:a24 $atom:a25 $atom:a26 $atom:a27 + $dihedral:d24b @dihedral:alpha2 $atom:a24 $atom:a25 $atom:a26 $atom:a27 + } + + # All consecutively bonded triplets of atoms same 3-body bond-angle + # interaction parameters. Of coarse, we could specify them all explicitly + # (as we did for the dihedrals above), but I wanted to show how to specify + # angles by atom type instead. (You can do this for dihedrals & impropers + # also.) + + # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type + + write_once("Data Angles By Type") { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # (The "*" is a wildcard character. I use "*" to denote any atom-type or + # bond-type which is defined within the current namespace: 1beadUnfrustrated) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 + pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 + pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 + } + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond-Type bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 100.0 1.0 + } + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # angle-Type anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 13.3333333333 105.0 + } + + # 4-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Udihedral(phi) = K * (1 + cos(n*phi - d)) + # + # The d parameter is in degrees, K is in kcal/mol/rad^2. + # + # The corresponding command is: + # + # dihedral_coeff dihedralType dihedralstylename K n d w + # ("w" is the weight for 1-4 pair interactions, which we set to 0) + + # NOTE: Currently, dihedral_coeff charmm does not allow non-integer d + # parameters. I'm hoping this will be fixed eventually. + + write_once("In Settings") { + # Correct version: + #dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57.2957795 0.0 + # Replacing with + dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57 0.0 + # Correct version: + #dihedral_coeff @dihedral:alpha2 charmm 0.375 2 114.591559 0.0 + # Replacing with + dihedral_coeff @dihedral:alpha2 charmm 0.375 2 115 0.0 + dihedral_coeff @dihedral:beta1 charmm -1.5 1 180 0.0 + dihedral_coeff @dihedral:beta2 charmm 0.375 2 360 0.0 + dihedral_coeff @dihedral:turn1 charmm -3.0 1 90 0.0 + # Correct version: + # dihedral_coeff @dihedral:turn2 charmm -3.0 1 11.4591559 0.0 + # Replacing with + dihedral_coeff @dihedral:turn2 charmm -3.0 1 11 0.0 + dihedral_coeff @dihedral:turn3 charmm -3.0 1 -90 0.0 + dihedral_coeff @dihedral:turn4 charmm 0.0 1 0 0.0 + dihedral_coeff @dihedral:turn5 charmm 0.0 1 0 0.0 + } + + write_once("In Settings") { + # Optional: define the atoms in the "proteins" group + group proteins type @atom:B + group proteins type @atom:L + group proteins type @atom:N + } + + # LAMMPS has many available force field styles (and atom styles). + # Here, we pick the ones which work well for this molecular model: + + write_once("In Init") { + # --- Default options for the "1BeadUnfrustrated" protein model --- + # --- (These can be overridden later.) --- + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid charmm + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + +} # 1beadUnfrustrated + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt new file mode 100644 index 000000000..cbc8fe217 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt @@ -0,0 +1,45 @@ +import "1beadUnfrustrated.lt" + + +# Alternate starting conformation (same molecule): + + +1beadUnfolded inherits 1beadUnfrustrated { + + # This molecule "inherits" all of its features from "1beadUnfrustrated" + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 + $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 + $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 + $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 + $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 + $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 + $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 + $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 + $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 + $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 + $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 + $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 + $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 + $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 + $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 + $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 + $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 + $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 + $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 + $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 + $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 + $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 + $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 + $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 + $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 + $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 + $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 + } + +} # 1beadUnfolded + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt new file mode 100644 index 000000000..8266d2a89 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt @@ -0,0 +1,41 @@ +# Here we define a trivial molecule containing only one particle. + +Chaperonin { + + # atomID molID atomType charge x y z + + write("Data Atoms") { + $atom:C $mol @atom:C 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:C 100.0 + } + + write_once("In Settings") { + # If for some reason there are multiple chaperones present, + # I assume that they interact repulsively (hence, L=0) + # i j epsilon sigma K L + + pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 6.0 1 0 + + # Optional: define the atoms in the "chaperonins" group: + # (Defining a group for the chaperone makes it easy to immobilize it later.) + + group chaperonins type @atom:C + } + + + # Specify which pair_styles, and atom styles work well with + # this model. (Again this can be overridden later.) + + write_once("In Init") { + units lj + atom_style full + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 11.0 12.0 + } + +} # Chaperonin + +# We have not specified how this particle interacts with other particles +# besides itself. Later on you must do this. diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py new file mode 100755 index 000000000..9b86809cc --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py @@ -0,0 +1,87 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between atoms in the +# protein and a chaperone provided in the supplemental materials section of: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# This is stored in a tabulated force field with a singularity at a distance R. +# +# To calculate the table for interaction between +# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181 +# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181 +# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True +# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True + +from math import * +import sys + +def U(r, eps, sigma, R, h): + #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h)) + # Formula is undefined at r=0, but you can take the limit: + if r <= 0: + return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0) + - h*pow((sigma/R), 6.0)) + xp = sigma/(r+R) + xm = sigma/(r-R) + term10 = pow(xm, 10.0) - pow(xp, 10.0) + term4 = pow(xm, 4.0) - pow(xp, 4.0) + return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4) + +def F(r, eps, sigma, R, h): + # Formula is undefined at r=0, but you can take the limit: + if r <= 0: + return 0.0 + product_term_a = U(r, eps, sigma, R, h) / r + ixp = (r+R)/sigma + ixm = (r-R)/sigma + dix_dr = 1.0/sigma + term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0)) + term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0)) + product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4) + return product_term_a + product_term_b + + +class InputError(Exception): + """ A generic exception object containing a string for error reporting. + + """ + def __init__(self, err_msg): + self.err_msg = err_msg + def __str__(self): + return self.err_msg + def __repr__(self): + return str(self) + +if len(sys.argv) < 8: + sys.stderr.write("Error: expected 7 arguments:\n" + "\n" + "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n") + sys.exit(-1) + +epsilon = float(sys.argv[1]) +sigma = float(sys.argv[2]) +R = float(sys.argv[3]) +h = float(sys.argv[4]) +rmin = float(sys.argv[5]) +rmax = float(sys.argv[6]) +N = int(sys.argv[7]) + +subtract_Urcut = False +if len(sys.argv) == 9: + subtract_Urcut = True +rcut = rmax + +for i in range(0,N): + r = rmin + i*(rmax-rmin)/(N-1) + U_r = U(r, epsilon, sigma, R, h) + F_r = F(r, epsilon, sigma, R, h) + if subtract_Urcut: + U_r -= U(rcut, epsilon, sigma, R, h) + if (r >= rcut) or (i==N-1): + U_r = 0.0 + F_r = 0.0 + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt new file mode 100644 index 000000000..d8781c26f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt @@ -0,0 +1,45 @@ +write_once("Data Boundary") { + 0.0 20.0 xlo xhi + 0.0 20.0 ylo yhi + 0.0 20.0 zlo zhi +} + + +import "chaperonin.lt" +import "1beadUnfrustrated_variants.lt" + + +chaperinin = new Chaperonin # (hollow chaperonin, encloses protein) +protein = new 1beadUnfolded # (unfolded conformation, unfrustrated protein) + + + +# Now define interactions between the "c" atom in the +# chaperone and the "B", "L", "N" atoms in the protein: + +write_once("In Settings") { + pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/B table table_chaperonin_h=0.dat CH_H0 + pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/L table table_chaperonin_h=0.dat CH_H0 + pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/N table table_chaperonin_h=0.dat CH_H0 + # Note: In this example, the chaperone is playing the role of a repulsive wall + # (confinement). To use a sticky chaperonin, replace the first line with this: + # pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/B table table_chaperonin_h=0.475.dat CH_H0.475 +} + + + +# LAMMPS has many available force field styles (and atom styles). +# Here, we pick the ones which work well for this molecular model: + +write_once("In Init") { + # --- Default options for the "1BeadUnfrustrated" protein model --- + # --- (These can be overridden later.) --- + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid charmm + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 1181 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) +} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat new file mode 100644 index 000000000..675d228a9 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat @@ -0,0 +1,1188 @@ +# Interaction between a chaperonin wall and hydrophobic ("B") beads (h=0.475). +# LAMMPS would crash unless I set the minimum radius to a positive value (not 0) + +CH_H0.475 +N 1181 R 0.00000000001 5.9 + +1 0.00000000001 -0.018422088583 0.0 +2 0.005 -0.0184221525389 2.55824082873e-05 +3 0.01 -0.0184223444081 5.11654127471e-05 +4 0.015 -0.018422664195 7.67496107175e-05 +5 0.02 -0.0184231119071 0.000102335598797 +6 0.025 -0.018423687555 0.000127923973785 +7 0.03 -0.0184243911519 0.000153515332637 +8 0.035 -0.0184252227143 0.000179110272379 +9 0.04 -0.0184261822615 0.000204709390236 +10 0.045 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b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat new file mode 100644 index 000000000..2ad6d7b69 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat @@ -0,0 +1,1187 @@ +# Interaction between a chaperonin wall and hydrophilic beads (type L or N, h=0) + +CH_H0 +N 1181 R 0.00000000001 5.9 + +1 0.00000000001 8.31299178857e-07 0.0 +2 0.005 8.31311879342e-07 -5.08022586688e-09 +3 0.01 8.31349981758e-07 -1.01608369733e-08 +4 0.015 8.31413488996e-07 -1.52422186449e-08 +5 0.02 8.31502405871e-07 -2.03247562721e-08 +6 0.025 8.31616739127e-07 -2.54088353865e-08 +7 0.03 8.31756497437e-07 -3.04948417048e-08 +8 0.035 8.319216914e-07 -3.55831611709e-08 +9 0.04 8.32112333547e-07 -4.06741800058e-08 +10 0.045 8.32328438343e-07 -4.57682847516e-08 +11 0.05 8.32570022183e-07 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-2.55154000294e+12 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min new file mode 100644 index 000000000..fce9843aa --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min @@ -0,0 +1,19 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt new file mode 100644 index 000000000..5fb8d71b3 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt @@ -0,0 +1,48 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.025 +dump 1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +# Keep the chaperonin fixed. Only let the protein move. + +fix fxlan proteins langevin 0.39 0.39 1.0 48279 +fix fxnve proteins nve + +# Notes: +# The temperature is in reduced units and is set to 0.39 +# which is the folding temperature for the unfrustrated protein. +# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, +# as it was in the paper. (Hopefully folding times should be similar.) +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 50 #(time interval for printing out "thermo" data) + +#restart 100000000 restart_nvt + +run 5000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT new file mode 100644 index 000000000..b2770e3e3 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT @@ -0,0 +1,27 @@ +# This directory demonstrates how to run a short simulation of +# the "unfrustrated" coarse-grained protein model used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) +# +# During this short simulation (run.in.nvt) the protein evolves +# from an unfolded initial conformation to the folded state. +# +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh new file mode 100755 index 000000000..45bd2d451 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh @@ -0,0 +1,31 @@ +# You would probably run lammps this way: +# +# lmp_ubuntu -i run.in.nvt + +# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer +# to the input scripts & data files you created earlier when you ran moltemplate +# system.in.init, system.in.settings, system.data + + + + +# ----------------------------------- + + + +LAMMPS_COMMAND="lmp_ubuntu" + +# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. + +# Run lammps using the following 3 commands: + +"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +"$LAMMPS_COMMAND" -i run.in.nvt # production run + +# Alternately, if you have MPI installed, try something like this: + +#NUMPROCS=4 +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh new file mode 100755 index 000000000..cb3196cf8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -overlay-dihdedrals system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt new file mode 100644 index 000000000..019afc144 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 000000000..1470af4bc --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,97 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 27 !NATOM + 1 1 2 2 0.000000 1.0000 0 + 2 1 1 1 0.000000 1.0000 0 + 3 1 2 2 0.000000 1.0000 0 + 4 1 1 1 0.000000 1.0000 0 + 5 1 2 2 0.000000 1.0000 0 + 6 1 1 1 0.000000 1.0000 0 + 7 1 3 3 0.000000 1.0000 0 + 8 1 3 3 0.000000 1.0000 0 + 9 1 1 1 0.000000 1.0000 0 + 10 1 2 2 0.000000 1.0000 0 + 11 1 1 1 0.000000 1.0000 0 + 12 1 2 2 0.000000 1.0000 0 + 13 1 1 1 0.000000 1.0000 0 + 14 1 2 2 0.000000 1.0000 0 + 15 1 3 3 0.000000 1.0000 0 + 16 1 3 3 0.000000 1.0000 0 + 17 1 3 3 0.000000 1.0000 0 + 18 1 1 1 0.000000 1.0000 0 + 19 1 1 1 0.000000 1.0000 0 + 20 1 2 2 0.000000 1.0000 0 + 21 1 2 2 0.000000 1.0000 0 + 22 1 1 1 0.000000 1.0000 0 + 23 1 1 1 0.000000 1.0000 0 + 24 1 2 2 0.000000 1.0000 0 + 25 1 2 2 0.000000 1.0000 0 + 26 1 1 1 0.000000 1.0000 0 + 27 1 2 2 0.000000 1.0000 0 + + 26 !NBOND: bonds + 1 2 2 3 3 4 4 5 + 5 6 6 7 7 8 8 9 + 9 10 10 11 11 12 12 13 + 13 14 14 15 15 16 16 17 + 17 18 18 19 19 20 20 21 + 21 22 22 23 23 24 24 25 + 25 26 26 27 + + 25 !NTHETA: angles + 13 14 15 7 8 9 6 7 8 + 16 17 18 15 16 17 2 3 4 + 4 5 6 9 10 11 11 12 13 + 14 15 16 1 2 3 3 4 5 + 10 11 12 12 13 14 25 26 27 + 5 6 7 8 9 10 17 18 19 + 18 19 20 22 23 24 21 22 23 + 19 20 21 20 21 22 23 24 25 + 24 25 26 + + 43 !NPHI: dihedrals + 1 2 3 4 1 2 3 4 + 2 3 4 5 2 3 4 5 + 3 4 5 6 3 4 5 6 + 4 5 6 7 4 5 6 7 + 5 6 7 8 6 7 8 9 + 7 8 9 10 8 9 10 11 + 8 9 10 11 9 10 11 12 + 9 10 11 12 10 11 12 13 + 10 11 12 13 11 12 13 14 + 11 12 13 14 12 13 14 15 + 12 13 14 15 13 14 15 16 + 14 15 16 17 15 16 17 18 + 15 16 17 18 16 17 18 19 + 16 17 18 19 17 18 19 20 + 17 18 19 20 18 19 20 21 + 18 19 20 21 19 20 21 22 + 19 20 21 22 20 21 22 23 + 20 21 22 23 21 22 23 24 + 21 22 23 24 22 23 24 25 + 22 23 24 25 23 24 25 26 + 23 24 25 26 24 25 26 27 + 24 25 26 27 + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg new file mode 100644 index 000000000..152fa88ff Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg new file mode 100644 index 000000000..bb269f47f Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt new file mode 100644 index 000000000..0dc1f5dd0 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt @@ -0,0 +1,255 @@ +# This file defines a pair of coarse-grained protein models used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) + + +1beadUnfrustrated { + + # Note: the "unfrustrated" model is kind of funny looking. (My apologies.) + + # There are 3 atom types (referred to above as B, L, and N) + # Define their masses: + + write_once("Data Masses") { + @atom:B 1.0 + @atom:L 1.0 + @atom:N 1.0 + } + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -1.3969548 1.7525716 -0.28565118 + $atom:a2 $mol @atom:B 0.0 -0.66847917 1.0738923 -0.39651074 + $atom:a3 $mol @atom:L 0.0 -0.16610379 1.0893417 0.44519456 + $atom:a4 $mol @atom:B 0.0 0.42244126 0.35006314 0.15979926 + $atom:a5 $mol @atom:L 0.0 1.2844393 0.55103218 0.64505356 + $atom:a6 $mol @atom:N 0.0 1.9703715 0.37775946 -0.05267634 + $atom:a7 $mol @atom:N 0.0 2.574926 -0.30399114 0.34330503 + $atom:a8 $mol @atom:N 0.0 2.029546 -1.1256647 0.19829852 + $atom:a9 $mol @atom:B 0.0 1.0936146 -0.76054936 0.1043528 + $atom:a10 $mol @atom:L 0.0 0.74888247 -0.81165991 1.0334863 + $atom:a11 $mol @atom:B 0.0 -0.069536333 -0.26815389 0.94356636 + $atom:a12 $mol @atom:L 0.0 -0.65671052 -0.522532 1.7113065 + $atom:a13 $mol @atom:N 0.0 -1.5278507 -0.10774689 1.4611921 + $atom:a14 $mol @atom:L 0.0 -2.1958878 -0.8403146 1.5521738 + $atom:a15 $mol @atom:N 0.0 -2.6058074 -0.86553455 0.64397232 + $atom:a16 $mol @atom:N 0.0 -1.8447588 -1.1286421 0.042924693 + $atom:a17 $mol @atom:N 0.0 -1.5328721 -0.28576244 -0.40564841 + $atom:a18 $mol @atom:B 0.0 -0.69593879 0.027664412 0.064884008 + $atom:a19 $mol @atom:B 0.0 0.0026517494 -0.66355162 -0.11470678 + $atom:a20 $mol @atom:L 0.0 -0.35479285 -1.2282381 -0.86455878 + $atom:a21 $mol @atom:L 0.0 -0.60202976 -0.47829758 -1.4411001 + $atom:a22 $mol @atom:B 0.0 -0.14616501 0.20157397 -0.87098365 + $atom:a23 $mol @atom:B 0.0 0.7755198 -0.14153019 -0.76838748 + $atom:a24 $mol @atom:L 0.0 1.2465693 0.19738595 -1.5794731 + $atom:a25 $mol @atom:L 0.0 0.77604792 1.0612244 -1.637442 + $atom:a26 $mol @atom:B 0.0 0.44801303 1.1110219 -0.6900789 + $atom:a27 $mol @atom:L 0.0 1.0908651 1.7386382 -0.24229241 + } + + # bond-ID bond-Type atom-ID atom-ID + + write("Data Bonds") { + $bond:b1 @bond:backbone $atom:a1 $atom:a2 + $bond:b2 @bond:backbone $atom:a2 $atom:a3 + $bond:b3 @bond:backbone $atom:a3 $atom:a4 + $bond:b4 @bond:backbone $atom:a4 $atom:a5 + $bond:b5 @bond:backbone $atom:a5 $atom:a6 + $bond:b6 @bond:backbone $atom:a6 $atom:a7 + $bond:b7 @bond:backbone $atom:a7 $atom:a8 + $bond:b8 @bond:backbone $atom:a8 $atom:a9 + $bond:b9 @bond:backbone $atom:a9 $atom:a10 + $bond:b10 @bond:backbone $atom:a10 $atom:a11 + $bond:b11 @bond:backbone $atom:a11 $atom:a12 + $bond:b12 @bond:backbone $atom:a12 $atom:a13 + $bond:b13 @bond:backbone $atom:a13 $atom:a14 + $bond:b14 @bond:backbone $atom:a14 $atom:a15 + $bond:b15 @bond:backbone $atom:a15 $atom:a16 + $bond:b16 @bond:backbone $atom:a16 $atom:a17 + $bond:b17 @bond:backbone $atom:a17 $atom:a18 + $bond:b18 @bond:backbone $atom:a18 $atom:a19 + $bond:b19 @bond:backbone $atom:a19 $atom:a20 + $bond:b20 @bond:backbone $atom:a20 $atom:a21 + $bond:b21 @bond:backbone $atom:a21 $atom:a22 + $bond:b22 @bond:backbone $atom:a22 $atom:a23 + $bond:b23 @bond:backbone $atom:a23 $atom:a24 + $bond:b24 @bond:backbone $atom:a24 $atom:a25 + $bond:b25 @bond:backbone $atom:a25 $atom:a26 + $bond:b26 @bond:backbone $atom:a26 $atom:a27 + } + + # (3-body) Angles are specified below + + # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. + # (These interactions are not determined by atom type.) + # + # Note that some quartets of atoms are listed because their + # potentials contain multiple terms in the Fourier expansion. + # (IE. multiple cosines... Be sure to use "-overlay-dihedrals"!) + # + # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID + + write("Data Dihedrals") { + $dihedral:d1a @dihedral:beta1 $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d1b @dihedral:beta2 $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d2a @dihedral:beta1 $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d2b @dihedral:beta2 $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d3a @dihedral:beta1 $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d3b @dihedral:beta2 $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d4a @dihedral:beta1 $atom:a4 $atom:a5 $atom:a6 $atom:a7 + $dihedral:d4b @dihedral:beta2 $atom:a4 $atom:a5 $atom:a6 $atom:a7 + $dihedral:d5 @dihedral:turn1 $atom:a5 $atom:a6 $atom:a7 $atom:a8 + $dihedral:d6 @dihedral:turn2 $atom:a6 $atom:a7 $atom:a8 $atom:a9 + $dihedral:d7 @dihedral:turn3 $atom:a7 $atom:a8 $atom:a9 $atom:a10 + $dihedral:d8a @dihedral:beta1 $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d8b @dihedral:beta2 $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d9a @dihedral:beta1 $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d9b @dihedral:beta2 $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d10a @dihedral:beta1 $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d10b @dihedral:beta2 $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d11a @dihedral:beta1 $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d11b @dihedral:beta2 $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d12a @dihedral:beta1 $atom:a12 $atom:a13 $atom:a14 $atom:a15 + $dihedral:d12b @dihedral:beta2 $atom:a12 $atom:a13 $atom:a14 $atom:a15 + $dihedral:d13 @dihedral:turn4 $atom:a13 $atom:a14 $atom:a15 $atom:a16 + $dihedral:d14 @dihedral:turn5 $atom:a14 $atom:a15 $atom:a16 $atom:a17 + $dihedral:d15a @dihedral:alpha1 $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d15b @dihedral:alpha2 $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d16a @dihedral:alpha1 $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d16b @dihedral:alpha2 $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d17a @dihedral:alpha1 $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d17b @dihedral:alpha2 $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d18a @dihedral:alpha1 $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d18b @dihedral:alpha2 $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d19a @dihedral:alpha1 $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d19b @dihedral:alpha2 $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d20a @dihedral:alpha1 $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d20b @dihedral:alpha2 $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d21a @dihedral:alpha1 $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d21b @dihedral:alpha2 $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d22a @dihedral:alpha1 $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d22b @dihedral:alpha2 $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d23a @dihedral:alpha1 $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d23b @dihedral:alpha2 $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d24a @dihedral:alpha1 $atom:a24 $atom:a25 $atom:a26 $atom:a27 + $dihedral:d24b @dihedral:alpha2 $atom:a24 $atom:a25 $atom:a26 $atom:a27 + } + + # All consecutively bonded triplets of atoms same 3-body bond-angle + # interaction parameters. Of coarse, we could specify them all explicitly + # (as we did for the dihedrals above), but I wanted to show how to specify + # angles by atom type instead. (You can do this for dihedrals & impropers + # also.) + + # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type + + write_once("Data Angles By Type") { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # (The "*" is a wildcard character. I use "*" to denote any atom-type or + # bond-type which is defined within the current namespace: 1beadUnfrustrated) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 + pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 + pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 + } + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond-Type bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 100.0 1.0 + } + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # angle-Type anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 13.3333333333 105.0 + } + + # 4-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Udihedral(phi) = K * (1 + cos(n*phi - d)) + # + # The d parameter is in degrees, K is in kcal/mol/rad^2. + # + # The corresponding command is: + # + # dihedral_coeff dihedralType dihedralstylename K n d w + # ("w" is the weight for 1-4 pair interactions, which we set to 0) + + # NOTE: Currently, dihedral_coeff charmm does not allow non-integer d + # parameters. I'm hoping this will be fixed eventually. + + write_once("In Settings") { + # Correct version: + #dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57.2957795 0.0 + # Replacing with + dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57 0.0 + # Correct version: + #dihedral_coeff @dihedral:alpha2 charmm 0.375 2 114.591559 0.0 + # Replacing with + dihedral_coeff @dihedral:alpha2 charmm 0.375 2 115 0.0 + dihedral_coeff @dihedral:beta1 charmm -1.5 1 180 0.0 + dihedral_coeff @dihedral:beta2 charmm 0.375 2 360 0.0 + dihedral_coeff @dihedral:turn1 charmm -3.0 1 90 0.0 + # Correct version: + # dihedral_coeff @dihedral:turn2 charmm -3.0 1 11.4591559 0.0 + # Replacing with + dihedral_coeff @dihedral:turn2 charmm -3.0 1 11 0.0 + dihedral_coeff @dihedral:turn3 charmm -3.0 1 -90 0.0 + dihedral_coeff @dihedral:turn4 charmm 0.0 1 0 0.0 + dihedral_coeff @dihedral:turn5 charmm 0.0 1 0 0.0 + } + + write_once("In Settings") { + # Optional: define the atoms in the "proteins" group + group proteins type @atom:B + group proteins type @atom:L + group proteins type @atom:N + } + + # LAMMPS has many available force field styles (and atom styles). + # Here, we pick the ones which work well for this molecular model: + + write_once("In Init") { + # --- Default options for the "1BeadUnfrustrated" protein model --- + # --- (These can be overridden later.) --- + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid charmm + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + +} # 1beadUnfrustrated + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt new file mode 100644 index 000000000..cbc8fe217 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt @@ -0,0 +1,45 @@ +import "1beadUnfrustrated.lt" + + +# Alternate starting conformation (same molecule): + + +1beadUnfolded inherits 1beadUnfrustrated { + + # This molecule "inherits" all of its features from "1beadUnfrustrated" + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 + $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 + $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 + $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 + $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 + $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 + $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 + $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 + $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 + $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 + $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 + $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 + $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 + $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 + $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 + $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 + $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 + $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 + $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 + $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 + $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 + $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 + $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 + $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 + $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 + $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 + $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 + } + +} # 1beadUnfolded + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt new file mode 100644 index 000000000..5ebe6efb8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt @@ -0,0 +1,11 @@ +import "1beadUnfrustrated_variants.lt" + + +protein = new 1beadUnfolded # (unfolded conformation, unfrustrated protein) + + +write_once("Data Boundary") { + 0.0 27.0 xlo xhi + 0.0 27.0 ylo yhi + 0.0 27.0 zlo zhi +} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min new file mode 100644 index 000000000..fce9843aa --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min @@ -0,0 +1,19 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt new file mode 100644 index 000000000..a831a97b4 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt @@ -0,0 +1,46 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.025 +dump 1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +fix fxlan all langevin 0.39 0.39 1.0 48279 +fix fxnve all nve + +# Notes: +# The temperature is in reduced units and is set to 0.39 +# which is the folding temperature for the unfrustrated protein. +# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, +# as it was in the paper. (Hopefully folding times should be similar.) +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 50 #(time interval for printing out "thermo" data) + +#restart 100000000 restart_nvt + +run 8000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README.TXT new file mode 100644 index 000000000..eda6a1ca2 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README.TXT @@ -0,0 +1,44 @@ +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. + +This is an example of a very simple coarse-grained protein. + +This example contains a 1-bead (C-alpha model) representation of the +"unfrustrated" 4-helix bundle model used in this paper: +G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) + +In this model, there are three atom-types (bead-types), H, L, and N +representing one amino-acid each. The "H" beads represent the hydrophobic +amino acids, and are attracted to eachother with a strength of "1.0" +(in dimensionless units of "epsilon"). The "L" and "N" atoms are +hydrophilic and purely repulsive, and only differ in their secondary-structure +propensity (ie their dihedral parameters). + +The dihedral-interaction is bi-stable with two deep local minima (corresponding +to helix-like and sheet-like secondary structure). You can adjust the bias +in favor of one minima or another by modifying the angle-shift parameter in +the appropriate "dihedral_coeff" command in the other .lt file. + +A definition for the 4-sheet beta-barell protein model is also included. +If you want to simulate that molecule instead, then edit the "system.lt" +file (in the "moltemplate_files" subdirectory), and replace this line: +prot = new 4HelixBundle + with +prot = new 4SheetBundle + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_run.sh new file mode 100755 index 000000000..45bd2d451 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_run.sh @@ -0,0 +1,31 @@ +# You would probably run lammps this way: +# +# lmp_ubuntu -i run.in.nvt + +# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer +# to the input scripts & data files you created earlier when you ran moltemplate +# system.in.init, system.in.settings, system.data + + + + +# ----------------------------------- + + + +LAMMPS_COMMAND="lmp_ubuntu" + +# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. + +# Run lammps using the following 3 commands: + +"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +"$LAMMPS_COMMAND" -i run.in.nvt # production run + +# Alternately, if you have MPI installed, try something like this: + +#NUMPROCS=4 +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_setup.sh new file mode 100755 index 000000000..cb3196cf8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -overlay-dihdedrals system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_visualize.txt new file mode 100644 index 000000000..019afc144 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg new file mode 100644 index 000000000..b4d919f9e Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg new file mode 100644 index 000000000..cd65146ff Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 000000000..de47509ed --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,214 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 73 !NATOM + 1 1 1 1 0.000000 1.0000 0 + 2 1 1 1 0.000000 1.0000 0 + 3 1 2 2 0.000000 1.0000 0 + 4 1 2 2 0.000000 1.0000 0 + 5 1 1 1 0.000000 1.0000 0 + 6 1 1 1 0.000000 1.0000 0 + 7 1 2 2 0.000000 1.0000 0 + 8 1 2 2 0.000000 1.0000 0 + 9 1 1 1 0.000000 1.0000 0 + 10 1 1 1 0.000000 1.0000 0 + 11 1 2 2 0.000000 1.0000 0 + 12 1 2 2 0.000000 1.0000 0 + 13 1 1 1 0.000000 1.0000 0 + 14 1 1 1 0.000000 1.0000 0 + 15 1 2 2 0.000000 1.0000 0 + 16 1 2 2 0.000000 1.0000 0 + 17 1 1 1 0.000000 1.0000 0 + 18 1 1 1 0.000000 1.0000 0 + 19 1 2 2 0.000000 1.0000 0 + 20 1 2 2 0.000000 1.0000 0 + 21 1 1 1 0.000000 1.0000 0 + 22 1 1 1 0.000000 1.0000 0 + 23 1 2 2 0.000000 1.0000 0 + 24 1 2 2 0.000000 1.0000 0 + 25 1 1 1 0.000000 1.0000 0 + 26 1 1 1 0.000000 1.0000 0 + 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47 48 71 72 63 64 73 72 + 14 15 16 65 30 31 32 67 + 46 47 48 71 62 63 64 73 + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt new file mode 100644 index 000000000..9b4ff2535 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt @@ -0,0 +1,274 @@ +# This file defines a family of coarse-grained protein models used in: +# G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) +# +# Strategy: +# +#1) First I'll define some building blocks (A16, B16, T3) +# which are helices, sheets and turns of a predetermined length) +# +#2) Then I'll copy and paste them together to build +# a 4-helix bundle or a 4-strand beta-barrel. +# This approach is optional. If your protein has helices which are not +# identical, you should probably just include all 4 helices in a single +# "Data Atoms" section and don't try to subdivide the protein into pieces.) + + +1beadProtSci2010 { # <-- enclose definitions in a namespace for portability + + write_once("In Init") { + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid fourier + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + + + # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) + + A16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../L 0.0 -0.4 -0.4 0.0 + $atom:a2 $mol:... @atom:../L 0.0 0.4 -0.4 0.6 + $atom:a3 $mol:... @atom:../H 0.0 0.4 0.4 1.2 + $atom:a4 $mol:... @atom:../H 0.0 -0.4 0.4 1.8 + $atom:a5 $mol:... @atom:../L 0.0 -0.4 -0.4 2.4 + $atom:a6 $mol:... @atom:../L 0.0 0.4 -0.4 3.0 + $atom:a7 $mol:... @atom:../H 0.0 0.4 0.4 3.6 + $atom:a8 $mol:... @atom:../H 0.0 -0.4 0.4 4.2 + $atom:a9 $mol:... @atom:../L 0.0 -0.4 -0.4 4.8 + $atom:a10 $mol:... @atom:../L 0.0 0.4 -0.4 5.4 + $atom:a11 $mol:... @atom:../H 0.0 0.4 0.4 6.0 + $atom:a12 $mol:... @atom:../H 0.0 -0.4 0.4 6.6 + $atom:a13 $mol:... @atom:../L 0.0 -0.4 -0.4 7.2 + $atom:a14 $mol:... @atom:../L 0.0 0.4 -0.4 7.8 + $atom:a15 $mol:... @atom:../H 0.0 0.4 0.4 8.4 + $atom:a16 $mol:... @atom:../H 0.0 -0.4 0.4 9.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # A16 + + + # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) + + B16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../L 0.0 -0.3 0.0 0.0 + $atom:a2 $mol:... @atom:../H 0.0 0.3 0.0 0.8 + $atom:a3 $mol:... @atom:../L 0.0 -0.3 0.0 1.6 + $atom:a4 $mol:... @atom:../H 0.0 0.3 0.0 2.4 + $atom:a5 $mol:... @atom:../L 0.0 -0.3 0.0 3.2 + $atom:a6 $mol:... @atom:../H 0.0 0.3 0.0 4.0 + $atom:a7 $mol:... @atom:../L 0.0 -0.3 0.0 4.8 + $atom:a8 $mol:... @atom:../H 0.0 0.3 0.0 5.6 + $atom:a9 $mol:... @atom:../L 0.0 -0.3 0.0 6.4 + $atom:a10 $mol:... @atom:../H 0.0 0.3 0.0 7.2 + $atom:a11 $mol:... @atom:../L 0.0 -0.3 0.0 8.0 + $atom:a12 $mol:... @atom:../H 0.0 0.3 0.0 8.8 + $atom:a13 $mol:... @atom:../L 0.0 -0.3 0.0 9.6 + $atom:a14 $mol:... @atom:../H 0.0 0.3 0.0 10.4 + $atom:a15 $mol:... @atom:../L 0.0 -0.3 0.0 11.2 + $atom:a16 $mol:... @atom:../H 0.0 0.3 0.0 12.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # B16 + + T3 { # T3 is a "turn" region consisting of 3 beads + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../N 0.0 -0.8 0.0 0.0 + $atom:a2 $mol:... @atom:../N 0.0 0.0 0.55 -0.24 + $atom:a3 $mol:... @atom:../N 0.0 0.8 0.0 0.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + } + + } # T3 + + # ----- Now build larger molecules using A16, B16 and T3 ------- + + 4SheetBarrel { + + sheet1 = new B16.rot( 45, 0,0,1).move(-0.793700526,-0.793700526, -6) + sheet2 = new B16.rot( 135, 0,0,1).move( 0.793700526,-0.793700526, -6) + sheet3 = new B16.rot( 225, 0,0,1).move( 0.793700526, 0.793700526, -6) + sheet4 = new B16.rot( 315, 0,0,1).move(-0.793700526, 0.793700526, -6) + + turn1 = new T3.rot(180,1,0,0).rot(0,0,0,1).move(0,-1.3,6.6) + turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(0.7,-0.0,-6.9) + turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move(0,1.3,6.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + 4HelixBundle { + + helix1 = new A16.rot( -45, 0,0,1).move(-1.12691645,-1.12691645, -4.5) + helix2 = new A16.rot( 45, 0,0,1).move( 1.12691645,-1.12691645, -4.5) + helix3 = new A16.rot( 135, 0,0,1).move( 1.12691645, 1.12691645, -4.5) + helix4 = new A16.rot( 225, 0,0,1).move(-1.12691645, 1.12691645, -4.5) + + turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-0.2,-0.7,5.4) + turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(0.7,-0.15,-4.8) + turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(0.2,0.7,5.4) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:H @atom:H lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 1.0 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 1.0 1.0 1 0 + } + # Interactions between different atoms use "repulsive wins" mixing rules + + + # bond_coeff bondType bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 66.6 1.0 + } + + + # angle_coeff angleType anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 66.6 105.0 + } + + # We use the same bond-angle forces whenever + # there are 3 consecutively-bonded atoms: + # + # angleType atomtypes1 2 3 bondtypes1 2 + + write_once("Data Angles By Type") { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + + + # From the Bellesia et al 2010 paper: + # for helices: U_{dih}(\phi) = 1.2*(cos(3\phi) + cos(\phi+\delta)) + # for turns: U_{dih}(\phi) = 0.2*cos(3\phi) + # + # General formula used for "dihedral_style fourier": + # U_{dih}(\phi) = \Sum_{i=1}^m K_i [ 1.0 + cos(n_i \phi - d_i) ] + # + # Syntax: + # dihedralType dihedralstyle m K_1 n_1 d_1 K2 n_2 d_2 ... + + write_once("In Settings") { + dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0 + dihedral_coeff @dihedral:delta62_5 fourier 2 2.167862 3 0 2.167862 1 -62.5 + dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0 + dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0 + # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon. + } + + + # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 + + write_once("Data Dihedrals By Type") { + @dihedral:delta60_0 @atom:H @atom:L @atom:H @atom:L * * * + @dihedral:delta60_0 @atom:H @atom:H @atom:L @atom:L * * * + @dihedral:delta60_0 @atom:H @atom:L @atom:L @atom:H * * * + @dihedral:delta60_0 @atom:L @atom:H @atom:H @atom:L * * * + @dihedral:turn @atom:N @atom:* @atom:* @atom:* * * * + } + # Note: This next rule is not needed: + # @dihedral:turn @atom:* @atom:* @atom:* @atom:N * * * + # (By reflection symmetry, it's equivalent to the rule above.) + # + # Note: The example in ../../membrane+protein/moltemplate_files/ + # demonstrates how to define dihedral angles for this model + # in an alternate way which might be easier to understand. + + + # --- Mass Units --- + # There are 3 atom types (referred to above as ../H, ../L, and ../N) + # Define their masses (in reduced units): + + write_once("Data Masses") { + @atom:H 1.0 + @atom:L 1.0 + @atom:N 1.0 + } + + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh new file mode 100755 index 000000000..852b9b76f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh @@ -0,0 +1,13 @@ +# run moltemplate this way + +moltemplate.sh system.lt + +# This will generate various files with names ending in *.in* and *.data +# which are needed by LAMMPS. + +# ------ Other versions: -------- +# +# If you are using the "other_versions/charmm/1beadProtSci2010.lt" file, +# then you must run moltemplate this way: +# +# moltemplate.sh -overlay-dihdedrals system.lt diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.TXT new file mode 100644 index 000000000..82bc8c5c4 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.TXT @@ -0,0 +1,13 @@ +This directory contains other versions of the same molecule +(with the same force-field), implemented in different ways. + +charmm/1beadProtSci2010.lt <-- This applies multiple "charmm" dihedral angle + forces to the same quartet of atoms to create + a Fourier series. (No packages needed.) + + NOTE: You must run moltemplate this way: + + moltemplate.sh -overlay-dihdedrals system.lt + +class2/1beadProtSci2010.lt <-- This uses the "class2" dihedral angles forces + (You must build LAMMPS with the CLASS2 package) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt new file mode 100644 index 000000000..d57186bee --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt @@ -0,0 +1,411 @@ +# This file defines a family of coarse-grained protein models used in: +# G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) +# +# +# For portability, all definitions in this file are enclosed within +# the "1beadProtSci2010" namespace. To access them, put +# "using namespace 1beadProtSci2010" in your LT file. + +# Strategy: +# +#1) First I'll define some building blocks +# (short helices, sheets and turns of a predetermined length) +# +#2) Then I'll cut and paste them together to build +# a 4-helix bundle or a 4-strand beta-barrel. +# +# Doing it this way is optional. It's simpler (but longer) to simply write +# out the entire sequence of all 73 atoms in a single "Data Atoms" section. +# (IE. Don't try to subdivide it.) It's also simpler to explicitly list the +# 72 bonds, 71 3-body angles and 70 4-body dihedral angle interactions +# manually (instead of inferring them from the atom type). If your protein +# has helices which are not identical, this would probably be easier. +# Use whichever style you prefer. +# +# +# Note that atom types, bond types, angle types, and dihedral types +# are shared between all molecules defined in the "1beadProtSci2010" family. +# (That's why there is a "../" in their path-names. Otherwise atom, bond, +# angle types, etc... are not shared between different molecules.) +# +# Confusing detail: +# Each molecule in LAMMPS can be assigned a unique molecule-ID (an integer). +# These are represented by the "$mol" variable written next to each atom. +# Our protein has multiple subunits (in this case: helices, sheets, turns). +# Because we want the subunits to share the same molecule-ID counter we use +# "$mol:..." instead of "$mol" which tells moltemplate to search for the +# parent molecule's ID. This is optional. If it bothers you, just use "$mol" + + + +1beadProtSci2010 { + + write_once("In Init") { + # -- Default styles for "1beadProtSci2010" -- + units lj + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid charmm + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + + # If charges are needed, (assuming biopolymers), try one of: + #dielectric 80.0 + #pair_style hybrid lj/cut/coul/debye 0.1 4.0 + # or (for short distances, below a couple nm) + #pair_style hybrid lj/charmm/coul/charmm/implicit 3.5 4.0 + + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + + + # ---- Building blocks: A16, B16, Turn3 ---- + + # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) + + A16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../L 0.0 -0.4 -0.4 0.0 + $atom:a2 $mol:... @atom:../L 0.0 0.4 -0.4 0.6 + $atom:a3 $mol:... @atom:../H 0.0 0.4 0.4 1.2 + $atom:a4 $mol:... @atom:../H 0.0 -0.4 0.4 1.8 + $atom:a5 $mol:... @atom:../L 0.0 -0.4 -0.4 2.4 + $atom:a6 $mol:... @atom:../L 0.0 0.4 -0.4 3.0 + $atom:a7 $mol:... @atom:../H 0.0 0.4 0.4 3.6 + $atom:a8 $mol:... @atom:../H 0.0 -0.4 0.4 4.2 + $atom:a9 $mol:... @atom:../L 0.0 -0.4 -0.4 4.8 + $atom:a10 $mol:... @atom:../L 0.0 0.4 -0.4 5.4 + $atom:a11 $mol:... @atom:../H 0.0 0.4 0.4 6.0 + $atom:a12 $mol:... @atom:../H 0.0 -0.4 0.4 6.6 + $atom:a13 $mol:... @atom:../L 0.0 -0.4 -0.4 7.2 + $atom:a14 $mol:... @atom:../L 0.0 0.4 -0.4 7.8 + $atom:a15 $mol:... @atom:../H 0.0 0.4 0.4 8.4 + $atom:a16 $mol:... @atom:../H 0.0 -0.4 0.4 9.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # A16 + + + # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) + + B16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../L 0.0 -0.3 0.0 0.0 + $atom:a2 $mol:... @atom:../H 0.0 0.3 0.0 0.8 + $atom:a3 $mol:... @atom:../L 0.0 -0.3 0.0 1.6 + $atom:a4 $mol:... @atom:../H 0.0 0.3 0.0 2.4 + $atom:a5 $mol:... @atom:../L 0.0 -0.3 0.0 3.2 + $atom:a6 $mol:... @atom:../H 0.0 0.3 0.0 4.0 + $atom:a7 $mol:... @atom:../L 0.0 -0.3 0.0 4.8 + $atom:a8 $mol:... @atom:../H 0.0 0.3 0.0 5.6 + $atom:a9 $mol:... @atom:../L 0.0 -0.3 0.0 6.4 + $atom:a10 $mol:... @atom:../H 0.0 0.3 0.0 7.2 + $atom:a11 $mol:... @atom:../L 0.0 -0.3 0.0 8.0 + $atom:a12 $mol:... @atom:../H 0.0 0.3 0.0 8.8 + $atom:a13 $mol:... @atom:../L 0.0 -0.3 0.0 9.6 + $atom:a14 $mol:... @atom:../H 0.0 0.3 0.0 10.4 + $atom:a15 $mol:... @atom:../L 0.0 -0.3 0.0 11.2 + $atom:a16 $mol:... @atom:../H 0.0 0.3 0.0 12.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # B16 + + T3 { # T3 is a "turn" region consisting of 3 beads + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../N 0.0 -0.8 0.0 0.0 + $atom:a2 $mol:... @atom:../N 0.0 0.0 0.55 -0.24 + $atom:a3 $mol:... @atom:../N 0.0 0.8 0.0 0.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + } + + } # T3 + + # (Note: Again, atom types, bond-types, (dihedral-types, any variable, etc) + # can be shared. The ".." in "@atom:../CA" tells moltemplate that + # atom type CA is defined in the parent's environment. (We are + # sharing the CA atom type between both the H and P residues. + # The same is true of the ".." in "@bond:../sidechain". + # + # + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # molecule's id number as it's own. + + + + # ----- Now build larger molecules using A16, B16 and T3 ------- + + 4HelixBundle { + + helix1 = new A16.rot( -45, 0,0,1).move(-1.12691645,-1.12691645, 0) + helix2 = new A16.rot( 45, 0,0,1).move( 1.12691645,-1.12691645, 0) + helix3 = new A16.rot( 135, 0,0,1).move( 1.12691645, 1.12691645, 0) + helix4 = new A16.rot( 225, 0,0,1).move(-1.12691645, 1.12691645, 0) + # Note: 1.12691645 ~= 0.5*2^(1/6) + 0.4*sqrt(2) + + turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-0.2,-0.7,9.9) + turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(0.7,-0.15,-0.3) + turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(0.2,0.7,9.9) + + # Note: In the paper, this is described as the "UA2" conformation + # (I played around with the angles until it looked "okay". This is not + # the minimum energy conformation. Further minimization is necessary.) + + # Now bond the pieces together. + # (Note: angle & dihedral interactions will be generated automatically.) + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # <-- create a variable for the parent's Molecule-ID + } + + 4SheetBundle { + + sheet1 = new B16.rot( 45, 0,0,1).move(-0.793700526,-0.793700526, 0) + sheet2 = new B16.rot( 135, 0,0,1).move( 0.793700526,-0.793700526, 0) + sheet3 = new B16.rot( 225, 0,0,1).move( 0.793700526, 0.793700526, 0) + sheet4 = new B16.rot( 315, 0,0,1).move(-0.793700526, 0.793700526, 0) + # Note: 0.793700526 ~= 0.5*2^(1/6) * sqrt(1/2) + + turn1 = new T3.rot(180,1,0,0).rot(0,0,0,1).move(0,-1.3,12.6) + turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(0.7,-0.0,-0.9) + turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move(0,1.3,12.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + # There are 3 atom types (referred to above as ../H, ../L, and ../N) + # Define their masses: + + write_once("Data Masses") { + @atom:H 1.0 + @atom:L 1.0 + @atom:N 1.0 + + } + + + + # -------------------------------------------------------------------- + # -- In this example, all force field parameters are stored in the -- + # -- file named "In Settings". They can also go in sections like -- + # -- "Data Pair Coeffs", "Data Bond Coeffs", "Data Angle Coeffs"... -- + # -------------------------------------------------------------------- + + + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:H @atom:H lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 1.0 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 1.0 1.0 1 0 + } + # (Interactions between different atom types use "arithmetic" + # and "maxmax" ("repulsion-wins") mixing rules.) + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond_coeff bondType bondstylename k r0 + # + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 66.6 1.0 + } + + + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # The corresponding command is: + # + # angle_coeff angleType anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 66.6 105.0 + } + + # Generate a "backbone" 3-body interaction whenever 3 atoms are bonded + # together. We do this by to asking moltemplate to generate this + # 3-body interaction whenever 3 consecutively bonded atoms satisfy + # the following type requirement: + # + # angleType atomtypes1 2 3 bondtypes1 2 + + write_once("Data Angles By Type") { + @angle:backbone * * * * * + } + + + + + + # 4-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Udihedral(phi) = K * (1 + cos(n*phi - d)) + # + # The d parameter is in degrees, K is in kcal/mol/rad^2. + # + # The corresponding command is: + # + # dihedral_coeff dihedralType dihedralstylename K n d w + # ("w" is the weight for 1-4 pair interactions, which we set to 0) + + write_once("In Settings") { + dihedral_coeff @dihedral:turn charmm 0.2 3 0 0 + dihedral_coeff @dihedral:term3 charmm 1.2 3 0 0 + + dihedral_coeff @dihedral:delta65_0 charmm 1.2 1 -65 0 + dihedral_coeff @dihedral:delta62_5 charmm 1.2 1 -62 0 + dihedral_coeff @dihedral:delta60_0 charmm 1.2 1 -60 0 + dihedral_coeff @dihedral:delta57_5 charmm 1.2 1 -57 0 + dihedral_coeff @dihedral:delta55_0 charmm 1.2 1 -55 0 + } + + #write_once("In Settings") { + # dihedral_coeff @dihedral:turn charmm 0.2 3 0.0 0 + # dihedral_coeff @dihedral:term3 charmm 1.2 3 0.0 0 + # dihedral_coeff @dihedral:delta65_0 charmm 1.2 1 -65.0 0 + # dihedral_coeff @dihedral:delta62_5 charmm 1.2 1 -62.5 0 + # dihedral_coeff @dihedral:delta60_0 charmm 1.2 1 -60.0 0 + # dihedral_coeff @dihedral:delta57_5 charmm 1.2 1 -57.5 0 + # dihedral_coeff @dihedral:delta55_0 charmm 1.2 1 -55.5 0 + #} + + # Generate 4-body interactions whenever 4 consecutively bonded atoms satisfy + # the following type requirements: + + write_once("Data Dihedrals By Type") { + # The dihedral interaction between backbone atoms in the helix or sheet-like + # regions is proportional to the sum of two terms: cos(phi+delta)+cos(3*phi) + # where delta is a constant used to control the bias between helices/sheets. + # As of 2013-4-07, the "fourier", "table", "class2", and "charmm", + " dihedral_styles can implement this potential. + # However dihedral_style "charmm" can only handle one cosine term at a time. + # So we use two commands to create two dihedral interactions for the same + # set of of four atoms ("cos3" and "delta60_0"). (To allow the + # superposition of multiple dihedral interactions on the same atoms, + # be sure to run moltemplate with the "-overlay-dihdedrals" argument.) + # + # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 + + @dihedral:term3 @atom:H @atom:L @atom:H @atom:L * * * + @dihedral:delta60_0 @atom:H @atom:L @atom:H @atom:L * * * + + @dihedral:term3 @atom:H @atom:L @atom:L @atom:H * * * + @dihedral:delta60_0 @atom:H @atom:L @atom:L @atom:H * * * + + @dihedral:term3 @atom:L @atom:H @atom:H @atom:L * * * + @dihedral:delta60_0 @atom:L @atom:H @atom:H @atom:L * * * + + @dihedral:term3 @atom:H @atom:H @atom:L @atom:L * * * + @dihedral:delta60_0 @atom:H @atom:H @atom:L @atom:L * * * + + # Comment out the next 4 lines: (They are redundant with the lines above) + #@dihedral:term3 @atom:L @atom:L @atom:H @atom:H * * * + #@dihedral:delta60_0 @atom:L @atom:L @atom:H @atom:H * * * + #@dihedral:term3 @atom:L @atom:H @atom:L @atom:H * * * + #@dihedral:delta60_0 @atom:L @atom:H @atom:L @atom:H * * * + # (Redundant: The LLHH pattern is identical to HHLL after order reversal) + # (Redundant: The LHLH pattern is identical to HLHL after order reversal) + + # Right now the dihedral-angle settings are "unfrustrated", meaning that the + # peptide backbone is equally happy to adopt helical or sheet-like secondary + # structure (See Table IV of Bellesia et. al, Prot Sci, 19, 141 (2010)). + # You can change that by changing "delta60_0" to one of the other choices. + + # Any dihedral interactions containing "N" atoms use the @dihedral:turn + # interaction (which is much weaker). + @dihedral:turn @atom:N @atom:* @atom:* @atom:* * * * + @dihedral:turn @atom:N @atom:N @atom:* @atom:* * * * + @dihedral:turn @atom:N @atom:N @atom:N @atom:* * * * + @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * + # Comment out the next 4 lines: (They are redundant with the lines above) + # @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * + # @dihedral:turn @atom:* @atom:N @atom:N @atom:N * * * + # @dihedral:turn @atom:* @atom:* @atom:N @atom:N * * * + # @dihedral:turn @atom:* @atom:* @atom:* @atom:N * * * + } + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt new file mode 100644 index 000000000..a0e305f84 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt @@ -0,0 +1,385 @@ +# This file defines a family of coarse-grained protein models used in: +# G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) +# +# +# For portability, all definitions in this file are enclosed within +# the "1beadProtSci2010" namespace. To access them, put +# "using namespace 1beadProtSci2010" in your LT file. + +# Strategy: +# +#1) First I'll define some building blocks +# (short helices, sheets and turns of a predetermined length) +# +#2) Then I'll cut and paste them together to build +# a 4-helix bundle or a 4-strand beta-barrel. +# +# Doing it this way is optional. It's simpler (but longer) to simply write +# out the entire sequence of all 73 atoms in a single "Data Atoms" section. +# (IE. Don't try to subdivide it.) It's also simpler to explicitly list the +# 72 bonds, 71 3-body angles and 70 4-body dihedral angle interactions +# manually (instead of inferring them from the atom type). If your protein +# has helices which are not identical, this would probably be easier. +# Use whichever style you prefer. +# +# +# Note that atom types, bond types, angle types, and dihedral types +# are shared between all molecules defined in the "1beadProtSci2010" family. +# (That's why there is a "../" in their path-names. Otherwise atom, bond, +# angle types, etc... are not shared between different molecules.) +# +# Confusing detail: +# Each molecule in LAMMPS can be assigned a unique molecule-ID (an integer). +# These are represented by the "$mol" variable written next to each atom. +# Our protein has multiple subunits (in this case: helices, sheets, turns). +# Because we want the subunits to share the same molecule-ID counter we use +# "$mol:..." instead of "$mol" which tells moltemplate to search for the +# parent molecule's ID. This is optional. If it bothers you, just use "$mol" + + + +1beadProtSci2010 { + + write_once("In Init") { + # -- Default styles for "1beadProtSci2010" -- + units lj + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid class2 + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 rsoftcore 1 + + # If charges are needed, (assuming biopolymers), try one of: + #dielectric 80.0 + #pair_style hybrid lj/cut/coul/debye 0.1 4.0 + # or (for short distances, below a couple nm) + #pair_style hybrid lj/charmm/coul/charmm/implicit 3.5 4.0 + + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + + + # ---- Building blocks: A16, B16, Turn3 ---- + + # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) + + A16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../L 0.0 -0.4 -0.4 0.0 + $atom:a2 $mol:... @atom:../L 0.0 0.4 -0.4 0.6 + $atom:a3 $mol:... @atom:../H 0.0 0.4 0.4 1.2 + $atom:a4 $mol:... @atom:../H 0.0 -0.4 0.4 1.8 + $atom:a5 $mol:... @atom:../L 0.0 -0.4 -0.4 2.4 + $atom:a6 $mol:... @atom:../L 0.0 0.4 -0.4 3.0 + $atom:a7 $mol:... @atom:../H 0.0 0.4 0.4 3.6 + $atom:a8 $mol:... @atom:../H 0.0 -0.4 0.4 4.2 + $atom:a9 $mol:... @atom:../L 0.0 -0.4 -0.4 4.8 + $atom:a10 $mol:... @atom:../L 0.0 0.4 -0.4 5.4 + $atom:a11 $mol:... @atom:../H 0.0 0.4 0.4 6.0 + $atom:a12 $mol:... @atom:../H 0.0 -0.4 0.4 6.6 + $atom:a13 $mol:... @atom:../L 0.0 -0.4 -0.4 7.2 + $atom:a14 $mol:... @atom:../L 0.0 0.4 -0.4 7.8 + $atom:a15 $mol:... @atom:../H 0.0 0.4 0.4 8.4 + $atom:a16 $mol:... @atom:../H 0.0 -0.4 0.4 9.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # A16 + + + # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) + + B16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../L 0.0 -0.3 0.0 0.0 + $atom:a2 $mol:... @atom:../H 0.0 0.3 0.0 0.8 + $atom:a3 $mol:... @atom:../L 0.0 -0.3 0.0 1.6 + $atom:a4 $mol:... @atom:../H 0.0 0.3 0.0 2.4 + $atom:a5 $mol:... @atom:../L 0.0 -0.3 0.0 3.2 + $atom:a6 $mol:... @atom:../H 0.0 0.3 0.0 4.0 + $atom:a7 $mol:... @atom:../L 0.0 -0.3 0.0 4.8 + $atom:a8 $mol:... @atom:../H 0.0 0.3 0.0 5.6 + $atom:a9 $mol:... @atom:../L 0.0 -0.3 0.0 6.4 + $atom:a10 $mol:... @atom:../H 0.0 0.3 0.0 7.2 + $atom:a11 $mol:... @atom:../L 0.0 -0.3 0.0 8.0 + $atom:a12 $mol:... @atom:../H 0.0 0.3 0.0 8.8 + $atom:a13 $mol:... @atom:../L 0.0 -0.3 0.0 9.6 + $atom:a14 $mol:... @atom:../H 0.0 0.3 0.0 10.4 + $atom:a15 $mol:... @atom:../L 0.0 -0.3 0.0 11.2 + $atom:a16 $mol:... @atom:../H 0.0 0.3 0.0 12.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # B16 + + T3 { # T3 is a "turn" region consisting of 3 beads + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../N 0.0 -0.8 0.0 0.0 + $atom:a2 $mol:... @atom:../N 0.0 0.0 0.55 -0.24 + $atom:a3 $mol:... @atom:../N 0.0 0.8 0.0 0.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + } + + } # T3 + + # (Note: Again, atom types, bond-types, (dihedral-types, any variable, etc) + # can be shared. The ".." in "@atom:../CA" tells moltemplate that + # atom type CA is defined in the parent's environment. (We are + # sharing the CA atom type between both the H and P residues. + # The same is true of the ".." in "@bond:../sidechain". + # + # + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # molecule's id number as it's own. + + + + # ----- Now build larger molecules using A16, B16 and T3 ------- + + 4HelixBundle { + + helix1 = new A16.rot( -45, 0,0,1).move(-1.12691645,-1.12691645, 0) + helix2 = new A16.rot( 45, 0,0,1).move( 1.12691645,-1.12691645, 0) + helix3 = new A16.rot( 135, 0,0,1).move( 1.12691645, 1.12691645, 0) + helix4 = new A16.rot( 225, 0,0,1).move(-1.12691645, 1.12691645, 0) + # Note: 1.12691645 ~= 0.5*2^(1/6) + 0.4*sqrt(2) + + turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-0.2,-0.7,9.9) + turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(0.7,-0.15,-0.3) + turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(0.2,0.7,9.9) + + # Note: In the paper, this is described as the "UA2" conformation + # (I played around with the angles until it looked "okay". This is not + # the minimum energy conformation. Further minimization is necessary.) + + # Now bond the pieces together. + # (Note: angle & dihedral interactions will be generated automatically.) + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # <-- create a variable for the parent's Molecule-ID + } + + 4SheetBundle { + + sheet1 = new B16.rot( 45, 0,0,1).move(-0.793700526,-0.793700526, 0) + sheet2 = new B16.rot( 135, 0,0,1).move( 0.793700526,-0.793700526, 0) + sheet3 = new B16.rot( 225, 0,0,1).move( 0.793700526, 0.793700526, 0) + sheet4 = new B16.rot( 315, 0,0,1).move(-0.793700526, 0.793700526, 0) + # Note: 0.793700526 ~= 0.5*2^(1/6) * sqrt(1/2) + + turn1 = new T3.rot(180,1,0,0).rot(0,0,0,1).move(0,-1.3,12.6) + turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(0.7,-0.0,-0.9) + turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move(0,1.3,12.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + # There are 3 atom types (referred to above as ../H, ../L, and ../N) + # Define their masses: + + write_once("Data Masses") { + @atom:H 1.0 + @atom:L 1.0 + @atom:N 1.0 + + } + + + + # -------------------------------------------------------------------- + # -- In this example, all force field parameters are stored in the -- + # -- file named "In Settings". They can also go in sections like -- + # -- "Data Pair Coeffs", "Data Bond Coeffs", "Data Angle Coeffs"... -- + # -------------------------------------------------------------------- + + + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:H @atom:H lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 0 0 0 0 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 1.0 1.0 1 0 0 0 0 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 1.0 1.0 1 0 0 0 0 0 + } + # (Interactions between different atom types use "arithmetic" + # and "maxmax" ("repulsion-wins") mixing rules.) + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond_coeff bondType bondstylename k r0 + # + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 66.6 1.0 + } + + + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # The corresponding command is: + # + # angle_coeff angleType anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 66.6 105.0 + } + + # Generate a "backbone" 3-body interaction whenever 3 atoms are bonded + # together. We do this by to asking moltemplate to generate this + # 3-body interaction whenever 3 consecutively bonded atoms satisfy + # the following type requirement: + # + # angleType atomtypes1 2 3 bondtypes1 2 + + write_once("Data Angles By Type") { + @angle:backbone * * * * * + } + + + + + + # 4-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Udihedral(phi) = K * (1 + cos(n*phi - d)) + # + # The d parameter is in degrees, K is in kcal/mol/rad^2. + # + # The corresponding command is: + # + + # From the Bellesia et al paper: Udihedral(x) = 1.2*(cos(x+delta) + cos(3x)) (delta=60) + # (scratchwork: 1.2*cos(x+60) = -1.2*cos(x+60-180) = -1.2*cos(x-120)) + # and 1.2*cos(3x) = -1.2*cos(3x-180) + # and 0.2*cos(x) = -0.2*cos(x - 180) + # This way, the energies match exactly with the implementation using charmm dihedrals.) + # + # dihedralType dihedralstylename K1 phi1 K2 phi2 K3 phi3 + + write_once("In Settings") { + dihedral_coeff @dihedral:delta60_0 class2 1.2 120.0 0 0 1.2 180.0 + dihedral_coeff @dihedral:turn class2 0 0 0 0 0.2 180.0 + + # All of the cross-terms (for the class2 force-field) are zero (see docs): + dihedral_coeff @dihedral:delta60_0 class2 mbt 0 0 0 0 + dihedral_coeff @dihedral:delta60_0 class2 ebt 0 0 0 0 0 0 0 0 + dihedral_coeff @dihedral:delta60_0 class2 at 0 0 0 0 0 0 0 0 + dihedral_coeff @dihedral:delta60_0 class2 aat 0 0 0 + dihedral_coeff @dihedral:delta60_0 class2 bb13 0 0 0 + dihedral_coeff @dihedral:turn class2 mbt 0 0 0 0 + dihedral_coeff @dihedral:turn class2 ebt 0 0 0 0 0 0 0 0 + dihedral_coeff @dihedral:turn class2 at 0 0 0 0 0 0 0 0 + dihedral_coeff @dihedral:turn class2 aat 0 0 0 + dihedral_coeff @dihedral:turn class2 bb13 0 0 0 + } + + # Generate 4-body interactions whenever 4 consecutively bonded atoms satisfy + # the following type requirements: + + write_once("Data Dihedrals By Type") { + # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 + + @dihedral:delta60_0 @atom:H @atom:L @atom:H @atom:L * * * + @dihedral:delta60_0 @atom:H @atom:H @atom:L @atom:L * * * + @dihedral:delta60_0 @atom:H @atom:L @atom:L @atom:H * * * + @dihedral:delta60_0 @atom:L @atom:H @atom:H @atom:L * * * + + @dihedral:turn @atom:N @atom:* @atom:* @atom:* * * * + @dihedral:turn @atom:N @atom:N @atom:* @atom:* * * * + @dihedral:turn @atom:N @atom:N @atom:N @atom:* * * * + @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * + + #### Comment out the next 6 lines: (They are redundant with the lines above) + ## @dihedral:delta60_0 @atom:L @atom:H @atom:L @atom:H * * * + ## @dihedral:delta60_0 @atom:L @atom:L @atom:H @atom:H * * * + ## @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * + ## @dihedral:turn @atom:* @atom:N @atom:N @atom:N * * * + ## @dihedral:turn @atom:* @atom:* @atom:N @atom:N * * * + ## @dihedral:turn @atom:* @atom:* @atom:* @atom:N * * * + ################################################################### + } + + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt new file mode 100644 index 000000000..6300c4ce3 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt @@ -0,0 +1,12 @@ +import "1beadProtSci2010.lt" + +using namespace 1beadProtSci2010 + +prot = new 4HelixBundle + +write_once("Data Boundary") { + 0 100 xlo xhi + 0 100 ylo yhi + 0 100 zlo zhi +} + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.min new file mode 100644 index 000000000..fce9843aa --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.min @@ -0,0 +1,19 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.nvt new file mode 100644 index 000000000..f1a7aa654 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.nvt @@ -0,0 +1,44 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.008 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +fix fxlan all langevin 0.4 0.4 1.0 48279 +fix fxnve all nve + +# Notes: +# The temperature is in reduced units and is set to 0.4. +# The inverse-damping-rate "damp" (which has units of time) is set to 1.0. +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 500 #(time interval for printing out "thermo" data) + +restart 10000000 restart_nvt + +run 1000000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README.TXT b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README.TXT new file mode 100644 index 000000000..305d00d63 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README.TXT @@ -0,0 +1,114 @@ + This example shows how to build a multicomponent spherical vesicle. + The lipid bilayer is composed of two different lipids (DPPC and DLPC). + The vesicle also contains trans-membrane protein inclusions. + + The coordinates for the vesicle are constructed by PACKMOL (see below). + + The DPPC lipid model is described here: + G. Brannigan, P.F. Philips, and F.L.H. Brown, + Physical Review E, Vol 72, 011915 (2005) + (The DLPC model is a truncated version of DPPC. Modifications discussed below.) + The protein model is described here: + G. Bellesia, AI Jewett, and J-E Shea, + Protein Science, Vol19 141-154 (2010) + +--- PREREQUISITES: --- + +1) This example requires PACKMOL. You can download PACKMOL here: + + http://www.ime.unicamp.br/~martinez/packmol/ + + (Moltemplate does not come with an easy way to generate spherically-symmetric + structures, so I used the PACKMOL program to move the molecules into position.) + +2) This example requires the "dihedral_style fourier", which is currently +in the USER-MISC package. Build LAMMPS with this package enabled using + make yes-user-misc +before compiling LAMMPS. +(See http://lammps.sandia.gov/doc/Section_start.html#start_3 for details.) + +3) This example may require additional features to be added to LAMMPS. +If LAMMPS complains about an "Invalid pair_style", then + a) download the "additional_lammps_code" from + http://moltemplate.org (upper-left corner menu) + b) unpack it + c) copy the .cpp and .h files to the src folding of your lammps installation. + d) (re)compile LAMMPS. + +------ Details ------- + +This example contains a coarse-grained model of a 4-helix bundle protein +inserted into a lipid bilayer (made from a mixture of DPPC and DLPC). + + -- Protein Model: -- + +The coarse-grained protein is described in: + G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) +Here we use the "AUF2" model described in that paper. +(The hydrophobic beads face outwards.) + + -- Memebrane Model: -- + +The DPPC lipid bilayer described in: + G. Brannigan, P.F. Philips, and F.L.H. Brown, + Physical Review E, Vol 72, 011915 (2005) +and: + M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown + J. Chem. Phys. 135, 244701 (2011) + +As in Watson(JCP 2011), rigid bond-length constraints +have been replaced by harmonic bonds. + +A truncated version of this lipid (named "DLPC") has also been added. +The bending stiffness of each lipid has been increased to compensate +for the additional disorder resulting from mixing two different types +of lipids together. (Otherwise pores appear.) +Unlike the original "DPPC" molecule model, the new "DPPC" and "DLPC" models +have not been carefully parameterized to reproduce the correct behavior in +a lipid bilayer mixture. + + -- Interactions between the proteins and lipids -- + +This is discussed in the "system.lt" file. + +--- Building the files necessary to run a simulation in LAMMPS --- + +step 1) Run PACKMOL + + Type these commands into the shell. + (Each command could take several hours.) + +cd packmol_files + packmol < step1_proteins.inp # This step determines the protein's location + packmol < step2_innerlayer.inp # this step builds the inner monolayer + packmol < step3_outerlayer.inp # this step builds the outer monolayer +cd .. + +step 2) Run MOLTEMPLATE + Type these commands into the shell. + (This could take up to 10 minutes.) + +cd moltemplate_files + moltemplate.sh system.lt -xyz ../system.xyz + mv -f system.in* system.data ../ + cp -f table_int.dat ../ +cd .. + +--- Running LAMMPS --- + +step3) Run LAMMPS: + Type these commands into the shell. + (This could take days.) + +lmp_linux -i run.in.min # Minimize the system (important, and very slow) + +lmp_linux -i run.in.nvt # Run a simulation at constant volume + +If you have compiled the MPI version of lammps, you can run lammps in parallel: + +mpirun -np 4 lmp_linux -i run.in.min + or +mpirun -np 4 lmp_linux -i run.in.nvt + +(Assuming you have 4 cores, for example.) + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_run.sh new file mode 100755 index 000000000..99f39891e --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_run.sh @@ -0,0 +1,24 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with MOLTEMPLATE and PACKMOL: +# system.in.init, system.in.settings, system.in.coords, system.data, +# and table_int.dat +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + +lmp_linux -i run.in.min # Minimize the system (important, and very slow) + +lmp_linux -i run.in.nvt # Run a simulation at constant volume + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.min +#or +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_setup.sh new file mode 100755 index 000000000..1ab21eb3e --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_setup.sh @@ -0,0 +1,50 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + +# First, generate the coordinates (the "system.xyz" file) this way +# (This can be a very slow process.) +cd packmol_files + + # You must run each packmol commend one after the other + # NOTE: If PACKMOL gets stuck in an endless loop, then edit the corresponding + # "inp" file. This should not happen. You can also usually interrupt + # packmol after 30 minutes, and the solution at that point should be good + # enough for use. + packmol < step1_proteins.inp # This step determines the protein's location + # It takes ~20 minutes (on an intel i7) + packmol < step2_innerlayer.inp # this step builds the inner monolayer + # It takes ~90 minutes + packmol < step3_outerlayer.inp # this step builds the outer monolayer + # It takes ~4 hours + + # Running these three commands will probably take about an hour. + # (It depends on how uniformly you need the packing to be.) + + mv -f step3_outerlayer.xyz ../system.xyz +cd .. + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -xyz ../system.xyz system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # The "table_int.dat" file contains tabular data for the lipid INT-INT atom + # 1/r^2 interaction. We need it too. (This slows down the simulation by x2, + # so I might look for a way to get rid of it later.) + cp -f table_int.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_visualize.txt new file mode 100644 index 000000000..019afc144 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/images/vesicle_membrane+protein_L.jpg b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/images/vesicle_membrane+protein_L.jpg new file mode 100644 index 000000000..c3ff59956 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/images/vesicle_membrane+protein_L.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010.lt new file mode 100644 index 000000000..d2aa805a5 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010.lt @@ -0,0 +1,233 @@ +# This file defines a 4-helix bundle coarse-grained protein model (AUF2) used in +# G. Bellesia, AI Jewett, and J-E Shea, +# Protein Science, Vol19 141-154 (2010) +# +# Strategy: +# +#1) First I'll define some building blocks (A16, B16, T3) +# which are helices, sheets and turns of a predetermined length) +# +#2) Then I'll copy and paste them together to build +# a 4-helix bundle (or a 4-strand beta-barrel). +# This approach is optional. If your protein has helices which are not +# identical, you should probably just include all 4 helices in a single +# "Data Atoms" section and don't try to subdivide the protein into pieces.) + + + +1beadProtSci2010 { # <-- enclose definitions in a namespace for portability + + # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) + + A16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../sL 0.0 -2.4 -2.4 0.0 + $atom:a2 $mol:... @atom:../sL 0.0 2.4 -2.4 3.6 + $atom:a3 $mol:... @atom:../sH 0.0 2.4 2.4 7.2 + $atom:a4 $mol:... @atom:../sH 0.0 -2.4 2.4 10.8 + $atom:a5 $mol:... @atom:../sL 0.0 -2.4 -2.4 14.4 + $atom:a6 $mol:... @atom:../sL 0.0 2.4 -2.4 18.0 + $atom:a7 $mol:... @atom:../sH 0.0 2.4 2.4 21.6 + $atom:a8 $mol:... @atom:../sH 0.0 -2.4 2.4 25.2 + $atom:a9 $mol:... @atom:../sL 0.0 -2.4 -2.4 28.8 + $atom:a10 $mol:... @atom:../sL 0.0 2.4 -2.4 32.4 + $atom:a11 $mol:... @atom:../sH 0.0 2.4 2.4 36.0 + $atom:a12 $mol:... @atom:../sH 0.0 -2.4 2.4 39.6 + $atom:a13 $mol:... @atom:../sL 0.0 -2.4 -2.4 43.2 + $atom:a14 $mol:... @atom:../sL 0.0 2.4 -2.4 46.8 + $atom:a15 $mol:... @atom:../sH 0.0 2.4 2.4 50.4 + $atom:a16 $mol:... @atom:../sH 0.0 -2.4 2.4 54.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # A16 + + + T3 { # T3 is a "turn" region consisting of 3 beads + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../tN 0.0 -4.8 0.0 0.0 + $atom:a2 $mol:... @atom:../tN 0.0 0.0 3.3 -1.44 + $atom:a3 $mol:... @atom:../tN 0.0 4.8 0.0 0.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + } + + } # T3 + + + # ----- Now build a larger molecule using A16 and T3 ------- + + # Create a 4-Helix bundle. + # In this version, the hydrophobic beads are poing outward. + # I oriented them this way because I want to place this protein in a membrane. + # (There is another file in this directory containing alternate version + # of this same molecule with the hydrophobic beads pointing inward.) + + 4HelixInsideOut { + helix1 = new A16.rot(-225, 0,0,1).move(-5.70,-5.70,-32.4) + helix2 = new A16.rot(-135, 0,0,1).move( 5.70,-5.70,-28.8) + helix3 = new A16.rot( -45, 0,0,1).move( 5.70, 5.70,-25.2) + helix4 = new A16.rot( 45, 0,0,1).move(-5.70, 5.70,-21.6) + + turn1 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot( 10,0,0,1).move(0.78,-4.2, 27.9) + turn2 = new T3.rot(-10,1,0,0).rot( 20,0,1,0).rot(-70,0,0,1).move(4.55, 2.4,-33.0) + turn3 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot(190,0,0,1).move(-0.78,4.2, 34.2) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixInsideOut + + + # -------- Minor coordinates adjustment: ----------- + + # Those coordinates in the commands above are a little too large. + # To make it easier to type them in, I was using sigma=6.0 Angstroms. + # Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667) + + 4HelixInsideOut.scale(0.9166666666666666) + + # Note: "scale()" only effects the initial coordinates of + # the molecule, not the force field parameters. + # (If you plan to minimize the molecule, you don't need to + # be so careful about the initial coordinates. In that case, + # you don't have worry about "scale()". Feel free to remove.) + + + + # -------------- Force-Field Parameters ------------ + + # Units and force-field styles for this protein model + # (These can be overridden later.) + + write_once("In Init") { + units real + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid fourier + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 21.0 24.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + + # --- Distance Units --- + # In this version of the model, sigma (the bond-length + # and particle diameter) is rounded to 5.5 Angstroms. + # + # --- Energy & Temperature Units --- + # In this protein model, "epsilon" represents the free energy + # bonus for bringing two hydrophobic amino acids together. + # Here I choose to set epsilon to 1.806551818181818 kCal/mole. + # This value was chosen so that a temperature of 300 Kelvin lies at + # 0.33 epsilon, which is the unfolding temperature of the marginally stable + # "ASF1" protein model from the Bellesia et al 2010 paper. + # This choice insures that both the "ASF1" model from that paper, + # as well as the much more stable "AUF2" protein we use here (which + # unfolds at 0.42*eps) should definitely remain stable at 300 degrees Kelvin, + # in the bulk at least. (However it's not clear that these energy + # parameters will work well for a protein in membrane. Perhaps I'll + # run some tests and fine tune these parameters for this scenario.) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:sH @atom:sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + pair_coeff @atom:sL @atom:sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 + pair_coeff @atom:tN @atom:tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 + } + + # The exact value of the bond_coeff does not matter too much as long as + # it is "stiff enough". Here I use a softer bond spring than the one + # used in the paper so that I can increase the time step. + # I also use a relatively soft spring to constrain the bond angles. + + # bond_coeff bondType bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:1beadProtSci2010/backbone harmonic 10.0 5.5 + } + + + # angleType atomtypes1 2 3 bondtypes1 2 + + write_once("Data Angles By Type") { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # angle_coeff angleType anglestylename k theta0 + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 100.0 105.0 + } + + + # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 + + write_once("Data Dihedrals By Type") { + # For a chain of sH and sL atoms, use the @dihedral:delta65_0 + # parameters. (This corresponds to the "AUF2" model from the + # Bellesia et. al 2010 paper.) + + @dihedral:delta65_0 @atom:s* @atom:s* @atom:s* @atom:s* * * * + + # If "tN" (turn) atoms are present, use the @dihedral:turn parameters + + @dihedral:turn @atom:tN @atom:* @atom:* @atom:* * * * + } + + write_once("In Settings") { + dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0 + dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0 + dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0 + # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon. + } + + + # --- Mass Units --- + # Typical amino acids weigh approximately 110.0 grams/mole. (Rounding down): + write_once("Data Masses") { + @atom:1beadProtSci2010/sH 100.0 + @atom:1beadProtSci2010/sL 100.0 + @atom:1beadProtSci2010/tN 100.0 + } + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010_variations.lt b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010_variations.lt new file mode 100644 index 000000000..e6e6bced7 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010_variations.lt @@ -0,0 +1,225 @@ +### THIS FILE IS OPTIONAL AND IS NOT NECESSARY. IN THIS FILE, I DEFINED SOME ## +### ADDITIONAL PROTEIN TYPES FROM THE PAPER THAT I DID NOT USE IN THIS EXAMPLE## +# +# This file defines a family of coarse-grained protein models used in: +# G. Bellesia, AI Jewett, and J-E Shea, +# Protein Science, Vol19 141-154 (2010) +# +# Strategy: +# +#1) First I'll define some building blocks (A16, B16, T3) +# which are helices, sheets and turns of a predetermined length) + +import "1beadProtSci2010.lt" + +# We defined A16 and T3 earlier in "1beadPRotSci2010.lt" Will define B16 below +# +#2) Then I'll copy and paste them together to build +# a 4-helix bundle or a 4-strand beta-barrel. + + +1beadProtSci2010 { #<-- Add new molecules to existing namespace defined earlier + # This way we don't have to start from scratch. We can + # use all the atom types and angle settings defined earlier + + # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) + + B16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../sL 0.0 -1.8 0.0 0.0 + $atom:a2 $mol:... @atom:../sH 0.0 1.8 0.0 4.8 + $atom:a3 $mol:... @atom:../sL 0.0 -1.8 0.0 9.6 + $atom:a4 $mol:... @atom:../sH 0.0 1.8 0.0 14.4 + $atom:a5 $mol:... @atom:../sL 0.0 -1.8 0.0 19.2 + $atom:a6 $mol:... @atom:../sH 0.0 1.8 0.0 24.0 + $atom:a7 $mol:... @atom:../sL 0.0 -1.8 0.0 28.8 + $atom:a8 $mol:... @atom:../sH 0.0 1.8 0.0 33.6 + $atom:a9 $mol:... @atom:../sL 0.0 -1.8 0.0 38.4 + $atom:a10 $mol:... @atom:../sH 0.0 1.8 0.0 43.2 + $atom:a11 $mol:... @atom:../sL 0.0 -1.8 0.0 48.0 + $atom:a12 $mol:... @atom:../sH 0.0 1.8 0.0 52.8 + $atom:a13 $mol:... @atom:../sL 0.0 -1.8 0.0 57.6 + $atom:a14 $mol:... @atom:../sH 0.0 1.8 0.0 62.4 + $atom:a15 $mol:... @atom:../sL 0.0 -1.8 0.0 67.2 + $atom:a16 $mol:... @atom:../sH 0.0 1.8 0.0 72.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # B16 + + # ----- Now build larger molecules using B16 and T3 ------- + + + 4SheetBarrel { + sheet1 = new B16.rot( 45, 0,0,1).move(-4.762203156,-4.762203156, -36.0) + sheet2 = new B16.rot( 135, 0,0,1).move( 4.762203156,-4.762203156, -36.0) + sheet3 = new B16.rot( 225, 0,0,1).move( 4.762203156, 4.762203156, -36.0) + sheet4 = new B16.rot( 315, 0,0,1).move(-4.762203156, 4.762203156, -36.0) + + turn1 = new T3.rot(180,1,0,0).rot( 0, 0,0,1).move( 0, -7.8, 39.6) + turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(4.2, 0.0,-41.4) + turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move( 0, 7.8, 39.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + # Below I define several alternate conformations of the"4HelixBundleInsideOut" + # molecule I defined earlier in "1beadProtSci2010.lt". Same molecule however. + + 4HelixBundle { + helix1 = new A16.rot( -45, 0,0,1).move(-5.70,-5.70,-32.4) + helix2 = new A16.rot( 45, 0,0,1).move( 5.70,-5.70,-28.8) + helix3 = new A16.rot( 135, 0,0,1).move( 5.70, 5.70,-25.2) + helix4 = new A16.rot( 225, 0,0,1).move(-5.70, 5.70,-21.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + + turn1 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot( 8,0,0,1).move(-3.6,-4.8,28.2) + turn2 = new T3.rot(-5,1,0,0).rot( 21,0,1,0).rot(-100,0,0,1).move(4.2,-0.66,-30.9) + turn3 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot(188,0,0,1).move(3.6,4.8,35.4) + + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixBundle + + + + + # --- alternate conformations (same molecule) ---- + + # In the following version, the helices are oriented in a similar way, + # but they are separated a little further away from eachother. + + 4HelixBundleLoose { + + helix1 = new A16.rot( -45, 0,0,1).move(-6.7347723,-6.7347723, -27.0) + helix2 = new A16.rot( 45, 0,0,1).move( 6.7347723,-6.7347723, -27.0) + helix3 = new A16.rot( 135, 0,0,1).move( 6.7347723, 6.7347723, -27.0) + helix4 = new A16.rot( 225, 0,0,1).move(-6.7347723, 6.7347723, -27.0) + + turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-1.2,-4.2,32.4) + turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(4.2,-0.9,-28.8) + turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(1.2,4.2,32.4) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + # In following version, the helices are oriented in a similar way, + # but they are separated a little further away from eachother. + + 4HelixInsideOutLoose { + helix1 = new A16.rot(-225, 0,0,1).move(-6.7347723,-6.7347723, -27.0) + helix2 = new A16.rot(-135, 0,0,1).move( 6.7347723,-6.7347723, -27.0) + helix3 = new A16.rot( -45, 0,0,1).move( 6.7347723, 6.7347723, -27.0) + helix4 = new A16.rot( 45, 0,0,1).move(-6.7347723, 6.7347723, -27.0) + + turn1 = new T3.rot(180,1,0,0).rot( 10,0,0,1).move( 0.78,-4.2,28.8) + turn2 = new T3.rot( 70,1,0,0).rot(-70,0,0,1).move( 10.8,2.4,-28.2) + turn3 = new T3.rot(180,1,0,0).rot(190,0,0,1).move(-0.78,4.2,28.8) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixInsideOutLoose + + + + + # In the following version, the 4 helices are arranged next to each other, + # side-by-side, in a planar conformation (instead of a compact bundle). + + 4HelixPlanar { + helix1 = new A16.rot(-00, 0,0,1).move(0, 0, -27.0) + helix2 = new A16.rot( 00, 0,0,1).move(14.4, 0, -27.0) + helix3 = new A16.rot(-00, 0,0,1).move(28.8, 0, -27.0) + helix4 = new A16.rot( 00, 0,0,1).move(43.2, 0, -27.0) + + turn1 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move( 4.8, 0, 31.8) + turn2 = new T3.rot( 0,1,0,0).rot(180,0,0,1).move(19.2, 0,-31.8) + turn3 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move(34.6, 0, 31.8) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixPlanar + + + # -------- Minor coordinates adjustment: ----------- + # Those coordinates in the commands above are a little too large. + # To make it easier to type them in, I was using sigma=6.0 Angstroms. + # Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667) + + 4SheetBarrel.scale(0.9166666666666666) + 4HelixBundle.scale(0.9166666666666666) + 4HelixBundleLoose.scale(0.9166666666666666) + 4HelixInsideOutLoose.scale(0.9166666666666666) + 4HelixPlanar.scale(0.9166666666666666) + + # Note: "scale()" only effects the initial coordinates of + # the molecule, not the force field parameters. + # (If you plan to minimize the molecule, you don't need to + # be so careful about the initial coordinates. In that case, + # you don't have worry about "scale()". Feel free to remove.) + + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt new file mode 100644 index 000000000..3b39048f7 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt @@ -0,0 +1,198 @@ +# Note: +# +# This example may require additional features to be added to LAMMPS. If +# LAMMPS complains about an "Invalid pair_style", then download copy the +# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS +# "src" directory and recompile LAMMPS. +# +# -------- Description -------- +# +# This example contains an implementation of the DPPC lipid bilayer described in +# G. Brannigan, P.F. Philips, and F.L.H. Brown, +# Physical Review E, Vol 72, 011915 (2005) +# and: +# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown +# J. Chem. Phys. 135, 244701 (2011) +# +# As in Watson(JCP 2011), rigid bond-length constraints have been replaced +# by harmonic bonds. +# +# A truncated version of this lipid (named "DLPC") has also been added. +# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully +# parameterized to reproduce the correct behavior in a lipid bilayer mixture. +# +# Units: +# +# The "epsilon" parameter in their model is approximately 2.75 kJ/mole +# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ) +# The "sigma" parameter corresponds to 7.5 angstroms. + + +CGLipidBr2005 { + + + write_once("In Init") { + # -- Default styles for "CGLipidBr2005" -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + + #angle_style hybrid cosine/delta # <- used in the original article + angle_style hybrid harmonic # <- prevents unphysical acute angle turns + # Explanation: + # angle_style cosine/delta: U(theta) = k*(1-cos(theta-theta0)) + # angle_style harmonic: U(theta) = k*(theta-theta0)^2 + + dihedral_style none + improper_style none + pair_style hybrid table linear 1130 & + lj/charmm/coul/charmm/inter es4k4l 14.5 15 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" + + neighbor 2.0 multi # <- perhaps unnecessary + communicate multi # <- perhaps unnecessary + } + + + DPPC { + write("Data Atoms") { + $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom + $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25 + $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75 + $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25 + $atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75 + } + write("Data Bonds") { + $bond:b1 @bond:../backbone $atom:h $atom:i + $bond:b2 @bond:../backbone $atom:i $atom:t1 + $bond:b3 @bond:../backbone $atom:t1 $atom:t2 + $bond:b4 @bond:../backbone $atom:t2 $atom:t3 + } + write("Data Angles") { + $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 + $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 + $angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3 + } + + # Define properties of the local (lipid-specific) atom:head type atom: + write_once("Data Masses") { + @atom:head 200.0 + } + write_once("In Settings") { + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + } + + } #DPPC + + + DLPC { + write("Data Atoms") { + $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom + $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50 + $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00 + $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50 + } + write("Data Bonds") { + $bond:b1 @bond:../backbone $atom:h $atom:i + $bond:b2 @bond:../backbone $atom:i $atom:t1 + $bond:b3 @bond:../backbone $atom:t1 $atom:t2 + } + write("Data Angles") { + $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 + $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 + } + # Define properties of the local (lipid-specific) atom:head type atom: + write_once("Data Masses") { + @atom:head 200.0 + } + write_once("In Settings") { + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + } + } #DLPC + + + # Particles and properties shared by all lipid types: + + write_once("Data Masses") { + @atom:int 200.0 + @atom:tail 200.0 + @atom:head 200.0 #<- Default head type. We may override it later. + } + + write_once("In Settings") { + # -- Default settings/parameters for "CGLipidBr2005" -- + # (Hybrid bond & angle styles were used for portability.) + + # As in Watson(JCP 2011), rigid bond-length constraints + # have been replaced by harmonic bonds. + # The k_theta parameter should lie in between 5*epsilon and 10*epsilon. + bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2 + } + + write_once("In Settings") { + # cosine/delta: U(theta) = k*(1-cos(theta-theta0)) + #angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps + # harmonic: U(theta) = k*(theta-theta0)^2 not (k/2)*(theta-theta0)^2 + angle_coeff @angle:backbone harmonic 9.85898661 180 #<-->30*eps + } + # I use a stiffer bond-angle than the original Brannigan & Brown 2005 paper + # to attempt to compensate for the fact that here we are using a lipid + # mixture of DPPC and DLPC. (The mixture of lipids introduces a great deal + # of disorder into the bilayer which would not be present in a DPPC bilayer. + # This causes pores to form. Increasing the angle stiffness prevents this.) + + write_once("In Settings") { + + # The interaction of "atom:int" with other "atom:int" atoms is given by + # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at + # r=3*sigma. This was implemented using pair_style table. + # Unfortunately, mixing lj/charmm and "table" pair styles in the same + # simulation is very inneficient. + + pair_coeff @atom:int @atom:int table table_int.dat INT + + # The interaction of tail beads with eachother is given by the formula below + # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules: + # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6), + pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + + # The interaction of head beads which all other beads is given by: + # epsilon*(0.4*(sigma/r)^12 - 0.0*(sigma/r)^6), + + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + + } # write_once("In Settings") + + # Note: I divided epsilon by 4 to get "0.1643" because we are using the + # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6) + # (The "es4k4l" coeffstyle is the default.) Using this convention makes it + # easier to mix this coarse-grained lipid model with other molecular models. + + + +} # CGLipidBr2005 + + + + + + + + +# Note: This example has not been optimized for speed. +# +# Unfortunately, using both lj/charmm and "table" pair styles in the same +# simulation seems to be very inneficient. (The simulation is twice as slow +# as using only the "lj/charmm" pair styles for every pairwise interaction, +# ...and about 25% slower than using "table" for every pairwise interaction. +# However the lennard-jones pair styles support mixing, so we use them to +# make it easier to run these molecules with other molecules which don't use +# pair_table. I felt that portability was worth the extra 25% slow down.) + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/README.sh new file mode 100755 index 000000000..df70396a7 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/README.sh @@ -0,0 +1,22 @@ +# This example shows how to build a multicomponent spherical vesicle. +# The lipid bilayer is composed of two different lipids (DPPC and DLPC), +# The vesicle contains 120 trans-membrane protein inclusions. +# +# ---------------- Prerequisites: ------------------ +# You must run packmol to generate the coordinates beforehand. +# Afterwards, move and rename the final coordinate file to "../system.xyz" +# To do this, check the README.sh file in the ../packmol_files directory. +# (or follow these instructions below) +# +# cd ../packmol_files +# packmol < step1_proteins.inp +# packmol < step2_innerlayer.inp +# packmol < step3_outerlayer.inp +# cp step3_outerlayer.xyz ../system.xyz +# +# These steps could take a few hours. +# +# --- After you have done that, you can run moltemplate using this command: --- + +moltemplate.sh -xyz ../system.xyz system.lt + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py new file mode 100755 index 000000000..0d09e4d02 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py @@ -0,0 +1,29 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between "INT" atoms +# in the lipid membrane model described in +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) +# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity) + +def U(r, eps, sigma): + return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) +def F(r, eps, sigma): + return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) + +epsilon = 2.75/4.184 # kCal/mole +sigma = 7.5 +Rmin = 0.02 +Rmax = 22.6 +rcut = 22.5 +N = 1130 + +for i in range(0,N): + r = Rmin + i*(Rmax-Rmin)/(N-1) + U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma) + F_r = F(r, epsilon, sigma) + if r > rcut: + U_r = 0.0 + F_r = 0.0 + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py new file mode 100755 index 000000000..32147e444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py @@ -0,0 +1,70 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between "INT" atoms +# in the lipid membrane model described in +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) +# I realized later this is not what we want because although energy is conserved +# all enrgies are shifted with respect to energies used in the Brannigan paper +# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole). +# (So don't use this.) + +# Calculate and print a + +def S(r, rc1, rc2, derivative=False): + """ + Calculate the switching function S(r) which decays continuously + between 1 and 0 in the range from rc1 to rc2 (rc2>rc1): + S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3 + I'm using the same smoothing/switching cutoff function used by the CHARMM + force-fields. (I'm even using the same code to implement it, taken + from lammps charmm/coul/charmm pair style, rewritten in python.) + + """ + assert(rc2>rc1) + rsq = r*r + rc1sq = rc1*rc1 + rc2sq = rc2*rc2 + denom_lj_inv = (1.0 / ((rc2sq-rc1sq)* + (rc2sq-rc1sq)* + (rc2sq-rc1sq))) + if rsq > rc2sq: + return 0.0 + elif rsq < rc1sq: + if derivative: + return 0.0 + else: + return 1.0 + else: + rc2sq_minus_rsq = (rc2sq - rsq) + rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq + if derivative: + return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv) + else: + return (rc2sq_minus_rsq_sq * + (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv) + + +def U(r, eps, sigma): + return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) + +def F(r, eps, sigma): + return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) + +epsilon = 2.75/4.184 # kCal/mole +sigma = 7.5 +Rmin = 0.02 +Rmax = 22.6 +Rc1 = 22.0 +Rc2 = 22.5 +N = 1130 + +for i in range(0,N): + r = Rmin + i*(Rmax-Rmin)/(N-1) + U_r = U(r, epsilon, sigma) + F_r = F(r, epsilon, sigma) + # Multiply U(r) & F(r) by the smoothing/switch function + U_r = U_r * S(r, Rc1, Rc2) + F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False) + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt new file mode 100644 index 000000000..98213116d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt @@ -0,0 +1,192 @@ +# Description: +# +# This example shows how to build a multicomponent spherical vesicle. +# The lipid bilayer is composed of two different lipids (DPPC and DLPC), +# The vesicle contains 120 trans-membrane protein inclusions. +# +# The DPPC lipid model is described here: +# G. Brannigan, P.F. Philips, and F.L.H. Brown, +# Physical Review E, Vol 72, 011915 (2005) +# The protein model is described here: +# G. Bellesia, AI Jewett, and J-E Shea, +# Protein Science, Vol19 141-154 (2010) +# The new DLPC model is a truncated version of DPPC, +# (Its behaviour has not been rigorously tested.) +# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to +# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293 +# +# NOTE: THE COORDINATES FOR THESE MOLECULES ARE GENERATED BY PACKMOL (see below) +# +# NOTE: +# This example may require additional features to be added to LAMMPS. +# If LAMMPS complains about an "Invalid pair_style", then copy the code +# in the "additional_lammps_code" directory into your LAMMPS "src" directory +# and recompile LAMMPS. + +# First, load the definitions of the molecules we will need: + +import "CGLipidBr2005.lt" +using namespace CGLipidBr2005 + +import "1beadProtSci2010.lt" +using namespace 1beadProtSci2010 + +# PREREQUISITES: +# Coordinates for the molecules in this example are loaded from an .XYZ file +# created by PACKMOL. This must be done in advance. (See ../packmol_files/) +# +# The XYZ file was created by PACKMOL in 3 steps: +# (Add the proteins, then pack lipids in the inner & outer layers around them.) +# +# step1) Creae 120 proteins. Distribute them on the surface of the sphere. +# +# step2) Keeping the coordinates from step1 fixed, +# a) first we add 9500 DPPC lipids to the inner monolayer +# b) then we add 9500 DLPC lipids to the inner monolayer +# +# step3) Keeping the coordinates from steps 1 and 2 fixed, +# a) first we add 12500 DPPC lipids to the outer monolayer +# b) then we add 12500 DLPC lipids to the outer monolayer +# +# The order that molecules are created in moltemplate should match the order +# they appear in the final XYZ file created by PACKMOL. (See above.) +# Consequently I instantiate the molecules in the same order here: + + +# Step 1) ---- protein inclusions ---- + +proteins = new 4HelixInsideOut [120] + +# Step 2a) ---- inner monolayer ---- +dppc_in = new DPPC [9500] +# Step 2b) +dlpc_in = new DLPC [9500] + +# Step 3a) ---- outer monolayer ---- +dppc_out = new DPPC [12500] +# Step 3b) +dlpc_out = new DLPC [12500] + + + +# ------------------ boundary conditions -------------------- + +write_once("Data Boundary") { + -500.0 500.0 xlo xhi + -500.0 500.0 ylo yhi + -500.0 500.0 zlo zhi +} + + +write_once("In Settings") { + + # ----------------------------------------------------------- + # -------- interactions between protein and lipids ---------- + # ----------------------------------------------------------- + + # Interactions between the protein and lipid atoms are usually + # determined by mixing rules. (However this is not possible some + # for atoms, such as the "int" atoms in the lipid model which + # interact using -1/r^2 attraction.) Mixing rules do not make + # sense for these atoms so we must explicitly define their + # interaction with all other atoms. + + # We want the hydrophobic interactions between hydrophobic residues in + # the protein and beads the interior of the lipid to be energetically + # similar to the attractive interactions between the lipid tails. + # + # Note: I made the width of the outward-facing protein beads slightly larger + # ("12.5") whenever they interact with the "tail" beads in each lipid + # (in order to make the protein wider there). + # This hopefully relieves some of the internal negative pressure in the center + # of the bilayer which can otherwise rip apart the protein or suck it into + # the bilaer. (This is a hack, and I'm not sure if it is necessary. + # For different protein or lipid models, you probably don't need this.) + # + # i j pairstylename eps sig K L + + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 12.5 0.4 -1 + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + + # To help keep the protein from tilting 90 degrees and burying itself + # within the lipid bilayer, we make the turn regions at either + # end of the protein (strongly) attracted to the head groups + # of the lipid. (In reality, they would probably be attracted + # to the water as well.) + + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + + # All other interactions between proteins and lipids are steric. + + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + + # ----------------------------------------------------------- + # -------- Modifications to the protein model: -------------- + # ----------------------------------------------------------- + # + # Turn off attraction between the hydrophobic "@atom:sH" beads: + # (These beads are located in the outside of a trans-membrane protein.) + + pair_coeff @atom:1beadProtSci2010/sH @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 + + # (Why: These beads are only attracted to + # each other in an aqueous environment) + + # ... and + # Turn ON attraction between the hydrophilic "@atom:sL" beads. + # (These beads are located in the interior of a trans-membrane protein.) + + pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + + # Why? + # In reality, polar groups in the interior of trans-membrane + # proteins do form hydrogen bonds with each other. This was + # absent from the original protein model because, in an aqueous + # environment, these groups preferentially interact with the water. + # + # Why is this necessary? + # Shouldn't attraction between lipid tails and the protein create + # an effective force which brings the hydrophilic beads together? + # (similar to the hydrophobic effect, but in reverse?). + # Answer: + # Unlike an aqueous environment (~zero pressure, or +1atm), there is + # a large negative pressure in the interior of some bilayer membrane + # models (such as this one). Without some kind of direct attraction + # between interior residues, the protein will get pulled apart. + # (Perhaps the attractive force I am using is too strong?) + +} + + +# Finally, we must combine the two force-field styles which were used for +# the coarse-grained lipid and protein. To do that, we write one last time +# to the "In Init" section. When reading the "Init" section LAMMPS will +# read these commands last and this will override any earlier settings. + +write_once("In Init") { + # -- These styles override earlier settings -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + angle_style hybrid cosine/delta harmonic + dihedral_style hybrid fourier + improper_style none + pair_style hybrid table linear 1130 lj/charmm/coul/charmm/inter es4k4l 14.5 15 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" + communicate multi +} + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/table_int.dat b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/table_int.dat new file mode 100644 index 000000000..b0d651d67 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/table_int.dat @@ -0,0 +1,1139 @@ +# Table for the INT-INT interaction from +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# This table contains +# i r_i U(r_i) -dU/dr|r_i +# where U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) + +INT +N 1130 + +1 0.02 2.0331818401e+30 1.21990910406e+33 +2 0.04 4.9638228518e+26 1.48914685554e+29 +3 0.06 3.82579033251e+24 7.65158066501e+26 +4 0.08 1.21187081343e+23 1.81780622014e+25 +5 0.1 8.32791281704e+21 9.99349538045e+23 +6 0.12 9.34030842897e+20 9.34030842897e+22 +7 0.14 1.46892540453e+20 1.25907891817e+22 +8 0.16 2.95866897809e+19 2.21900173357e+21 +9 0.18 7.19889946863e+18 4.79926631242e+20 +10 0.2 2.0331818401e+18 1.21990910406e+20 +11 0.22 6.47834392264e+17 3.53364213962e+19 +12 0.24 2.28034873754e+17 1.14017436877e+19 +13 0.26 8.72681951932e+16 4.02776285507e+18 +14 0.28 3.58624366341e+16 1.53696157003e+18 +15 0.3 1.56704372019e+16 6.26817488078e+17 +16 0.32 7.2233129348e+15 2.70874235055e+17 +17 0.34 3.48970861422e+15 1.23166186384e+17 +18 0.36 1.75754381558e+15 5.85847938527e+16 +19 0.38 9.18613895646e+14 2.90088598625e+16 +20 0.4 4.96382285179e+14 1.48914685554e+16 +21 0.42 2.76404230108e+14 7.89726371739e+15 +22 0.44 1.58162693423e+14 4.31352800247e+15 +23 0.46 9.27773983256e+13 2.42027995633e+15 +24 0.48 5.56725765996e+13 1.391814415e+15 +25 0.5 3.41111308981e+13 8.18667141564e+14 +26 0.52 2.13057117167e+13 4.91670270393e+14 +27 0.54 1.35459994024e+13 3.0102220895e+14 +28 0.56 8.75547769351e+12 1.87617379153e+14 +29 0.58 5.74645813711e+12 1.18892237325e+14 +30 0.6 3.8257903322e+12 7.65158066491e+13 +31 0.62 2.58128463312e+12 4.99603477424e+13 +32 0.64 1.7635041342e+12 3.30657025205e+13 +33 0.66 1.21901470178e+12 2.21639036726e+13 +34 0.68 8.51979641904e+11 1.50349348607e+13 +35 0.7 6.0167184547e+11 1.0314374497e+13 +36 0.72 4.29087845387e+11 7.15146409276e+12 +37 0.74 3.08855637556e+11 5.00846980094e+12 +38 0.76 2.24270970425e+11 3.54112058818e+12 +39 0.78 1.64210505205e+11 2.52631546702e+12 +40 0.8 1.2118708117e+11 1.81780621971e+12 +41 0.82 90109367359.1 1.31867367068e+12 +42 0.84 67481501334.4 9.64021449503e+11 +43 0.86 50880896383.4 7.09965997788e+11 +44 0.88 38613938681.2 5.26553710913e+11 +45 0.9 29486692086.8 3.93155896009e+11 +46 0.92 22650731882.4 2.95444330322e+11 +47 0.94 17498544395.3 2.23385674464e+11 +48 0.96 13591937526.4 1.69899220331e+11 +49 0.98 10612635712.6 1.29950642555e+11 +50 1.0 8327912706.34 99934953582.6 +51 1.02 6566502316.69 77252969474.2 +52 1.04 5201589672.36 60018343356.8 +53 1.06 4138717434.11 46853405843.3 +54 1.08 3307128665.58 36745874940.0 +55 1.1 2653529579.27 28947596241.1 +56 1.12 2137567708.15 22902511945.9 +57 1.14 1728534024.3 18195095739.0 +58 1.16 1402943799.0 14513212422.1 +59 1.18 1142752163.37 11621209113.9 +60 1.2 934030766.093 9340308300.6 +61 1.22 765981286.774 7534242773.65 +62 1.24 630196371.787 6098675145.29 +63 1.26 520103253.414 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b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/DLPC.xyz @@ -0,0 +1,6 @@ +4 + DLPC coarse-grained lipid + 4 0.000000 0.000000 30.000000 + 2 0.000000 0.000000 22.500000 + 3 0.000000 0.000000 15.000000 + 3 0.000000 0.000000 7.500000 diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/DPPC.xyz b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/DPPC.xyz new file mode 100644 index 000000000..c25a2dbd1 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/DPPC.xyz @@ -0,0 +1,7 @@ +5 + DPPC coarse-grained lipid + 1 0.000000 0.000000 33.750000 + 2 0.000000 0.000000 26.250000 + 3 0.000000 0.000000 18.750000 + 3 0.000000 0.000000 11.250000 + 3 0.000000 0.000000 3.750000 diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/README.sh b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/README.sh new file mode 100755 index 000000000..8df6285ca --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/README.sh @@ -0,0 +1,18 @@ +# Here we generate the starting coordinates of the simulation +# using PACKMOL + +# Running these three commands will probably take hours or even days. +# (It depends on how dense and how uniformly you need the packing to be.) +# NOTE: If PACKMOL gets stuck in an endless loop, then edit the corresponding +# "inp" file. This should not happen. You can also usually interrupt +# packmol after 30 minutes, and the solution at that point should be good +# enough for use. + +packmol < step1_proteins.inp # This step determines the protein's location + # It takes ~20 minutes (on an intel i7) +packmol < step2_innerlayer.inp # This step builds the inner monolayer + # It takes ~90 minutes +packmol < step3_outerlayer.inp # This step builds the outer monolayer + # It takes ~4 hours + +# This should create a file named "system.xyz" (which moltemplate will read). diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/protein.xyz b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/protein.xyz new file mode 100644 index 000000000..75557e6ff --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/protein.xyz @@ -0,0 +1,75 @@ +73 + +6 -2.11383 -5.225 -29.7 +6 -5.225 -2.11383 -26.4 +7 -8.33617 -5.225 -23.1 +7 -5.225 -8.33617 -19.8 +6 -2.11383 -5.225 -16.5 +6 -5.225 -2.11383 -13.2 +7 -8.33617 -5.225 -9.9 +7 -5.225 -8.33617 -6.6 +6 -2.11383 -5.225 -3.3 +6 -5.225 -2.11383 0 +7 -8.33617 -5.225 3.3 +7 -5.225 -8.33617 6.6 +6 -2.11383 -5.225 9.9 +6 -5.225 -2.11383 13.2 +7 -8.33617 -5.225 16.5 +7 -5.225 -8.33617 19.8 +6 5.225 -2.11383 -26.4 +6 2.11383 -5.225 -23.1 +7 5.225 -8.33617 -19.8 +7 8.33617 -5.225 -16.5 +6 5.225 -2.11383 -13.2 +6 2.11383 -5.225 -9.9 +7 5.225 -8.33617 -6.6 +7 8.33617 -5.225 -3.3 +6 5.225 -2.11383 0 +6 2.11383 -5.225 3.3 +7 5.225 -8.33617 6.6 +7 8.33617 -5.225 9.9 +6 5.225 -2.11383 13.2 +6 2.11383 -5.225 16.5 +7 5.225 -8.33617 19.8 +7 8.33617 -5.225 23.1 +6 2.11383 5.225 -23.1 +6 5.225 2.11383 -19.8 +7 8.33617 5.225 -16.5 +7 5.225 8.33617 -13.2 +6 2.11383 5.225 -9.9 +6 5.225 2.11383 -6.6 +7 8.33617 5.225 -3.3 +7 5.225 8.33617 0 +6 2.11383 5.225 3.3 +6 5.225 2.11383 6.6 +7 8.33617 5.225 9.9 +7 5.225 8.33617 13.2 +6 2.11383 5.225 16.5 +6 5.225 2.11383 19.8 +7 8.33617 5.225 23.1 +7 5.225 8.33617 26.4 +6 -5.225 2.11383 -19.8 +6 -2.11383 5.225 -16.5 +7 -5.225 8.33617 -13.2 +7 -8.33617 5.225 -9.9 +6 -5.225 2.11383 -6.6 +6 -2.11383 5.225 -3.3 +7 -5.225 8.33617 0 +7 -8.33617 5.225 3.3 +6 -5.225 2.11383 6.6 +6 -2.11383 5.225 9.9 +7 -5.225 8.33617 13.2 +7 -8.33617 5.225 16.5 +6 -5.225 2.11383 19.8 +6 -2.11383 5.225 23.1 +7 -5.225 8.33617 26.4 +7 -8.33617 5.225 29.7 +8 -3.35683 -4.56775 24.0698 +8 0.795667 -6.90708 26.8152 +8 4.78683 -3.13225 27.0802 +8 2.75642 6.08575 -28.7448 +8 6.54133 3.72717 -31.9651 +8 5.58525 -1.68575 -31.7552 +8 3.35683 4.56775 29.8448 +8 -0.795667 6.90708 32.5903 +8 -4.78683 3.13225 32.8552 diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step1_proteins.inp b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step1_proteins.inp new file mode 100644 index 000000000..abb48db7d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step1_proteins.inp @@ -0,0 +1,49 @@ +# Step 1: Create a sphere of proteins lying +# (In step 2 we will pack lipids around these proteins +# +# ----- Run using: ----- +# packmol < step1_proteins.inp +# (This takes about 30 minutes on an Intel i7 processor) + + +# ----- Settings: ----- + +# All the atoms from diferent proteins will be at least 50.0 Angstrons apart. +tolerance 50.0 +# (Setting "discale" to 2.0 increases the typical separation +# distance to approximately 2.0*50.0 = 100.0 Angstroms.) +discale 2.0 +# The other parameters below are optional: +nloop 10000 +maxit 20 +seed 12345 +sidemax 3000.0 +# What fraction of the molecules are moved during "large moves"? (default 0.05) +movefrac 0.05 + + +# The output file name + +output step1_proteins.xyz + + +# File types are in xyz format + +filetype xyz + + + +# First, specify the protein inclusions +# We will pack the lipids around these later + +structure protein.xyz + number 120 + atoms 68 69 70 + inside sphere 0. 0. 0. 273.75 + end atoms + atoms 65 66 67 71 72 73 + outside sphere 0. 0. 0. 325.0 + end atoms +end structure + + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step2_innerlayer.inp b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step2_innerlayer.inp new file mode 100644 index 000000000..9f61960f2 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step2_innerlayer.inp @@ -0,0 +1,70 @@ +# NOTE: YOU MUST COMPLETE STEP 1 BEFORE RUNNING PACKMOL ON THIS FILE + +# Step 2: Pack the lipids in the inner monolayer around the proteins from step1. +# +# ----- Run using: ----- +# packmol < step2_innerlayer.inp +# (This takes about 90 minutes on an Intel i7 processor) + + +# ----- Settings: ----- + +# All the atoms from diferent molecules will be at least 5.5 Angstrons apart +tolerance 5.5 +# (Setting "discale" to 1.4 increases the typical separation +# distance to approximately 1.4*5.5 = 7.7 Angstroms.) +discale 1.4 +# The other parameters below are optional: +nloop 10000 +maxit 20 +seed 12345 +sidemax 3000.0 +# What fraction of the molecules are moved during "large moves"? (default 0.05) +movefrac 0.05 + + +# The output file name + +output step2_innerlayer.xyz + +# File types are in xyz format + +filetype xyz + + +# The proteins whose position we determined earlier in step 1 +# will be frozen in place during this step. + +structure step1_proteins.xyz + number 1 + fixed 0. 0. 0. 0. 0. 0. +end structure + + +# 9500 DPPC lipids will be put in a shell with their hydrophilic heads +# (atom 1) pointing inwards, and their tails (atom 5) pointing outwards. + + +structure DPPC.xyz + number 9500 + atoms 1 + inside sphere 0. 0. 0. 270.0 + end atoms + atoms 5 + outside sphere 0. 0. 0. 295.0 + end atoms +end structure + +# 9500 DLPC lipids will be put in a shell with their hydrophilic heads +# (atom 1) pointing inwards, and their tails (atom 4) pointing outwards. + +structure DLPC.xyz + number 9500 + atoms 1 + inside sphere 0. 0. 0. 273.0 + end atoms + atoms 4 + outside sphere 0. 0. 0. 295.0 + end atoms +end structure + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step3_outerlayer.inp b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step3_outerlayer.inp new file mode 100644 index 000000000..bed1c0424 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step3_outerlayer.inp @@ -0,0 +1,70 @@ +# NOTE: YOU MUST COMPLETE STEPS 1 AND 2 BEFORE RUNNING PACKMOL ON THIS FILE + +# Step 3: Pack the lipids in the outer monolayer around the proteins from step1. +# +# ----- Run using: ----- +# packmol < step3_outerlayer.inp +# (This takes about 4 hours on an Intel i7 processor) + + +# ----- Settings: ----- + +# All the atoms from diferent molecules will be at least 5.5 Angstrons apart +tolerance 5.5 +# (Setting "discale" to 1.4 increases the typical separation +# distance to approximately 1.4*5.5 = 7.7 Angstroms.) +discale 1.4 +# The other parameters below are optional: +nloop 10000 +maxit 20 +seed 12345 +sidemax 3000.0 +# What fraction of the molecules are moved during "large moves"? (default 0.05) +movefrac 0.05 + + +# The output file name + +output step3_outerlayer.xyz + +# File types are in xyz format + +filetype xyz + + +# The proteins and lipids whose position we determined earlier in steps 1-2 +# will be frozen in place during this step. + +structure step2_innerlayer.xyz + number 1 + fixed 0. 0. 0. 0. 0. 0. +end structure + + +# 12500 DPPC lipids will be put in a shell with their hydrophilic heads +# (atom 1) pointing outwards, and their tails (atom 5) pointing inwards. + + +structure DPPC.xyz + number 12500 + atoms 5 + inside sphere 0. 0. 0. 310.0 + end atoms + atoms 1 + outside sphere 0. 0. 0. 336.0 + end atoms +end structure + +# 12500 DLPC lipids will be put in a shell with their hydrophilic heads +# (atom 1) pointing outwards, and their tails (atom 4) pointing inwards. + +structure DLPC.xyz + number 12500 + atoms 4 + inside sphere 0. 0. 0. 313.0 + end atoms + atoms 1 + outside sphere 0. 0. 0. 332.0 + end atoms +end structure + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.min b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.min new file mode 100644 index 000000000..9cb2d9300 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.min @@ -0,0 +1,46 @@ +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# So, after typing "make yes-user-misc" in to the shell, ... +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. +# +# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" +# then you made a mistake in the instructions above. + + + +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +# minimize + +minimize 1.0e-5 1.0e-7 5000 20000 + +# If minimization crashes, then instead try Langevin dynamics +# with a small timestep and a fast damping parameter. For example: +# +# timestep 0.05 +# fix fxlan all langevin 300.0 300.0 100.0 48279 +# fix fxnve all nve +# +# run 10000 + +write_data system_after_min.data diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.nvt new file mode 100644 index 000000000..253c04267 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.nvt @@ -0,0 +1,63 @@ +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# So, after typing "make yes-user-misc" in to the shell, ... +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. +# +# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" +# then you made a mistake in the instructions above. +# +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +# Commenting out: +# +# read_data system.data +# +# Instead read the data file created by "run.in.min". + +read_data system_after_min.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + +# Just in case the previous minimization failed, try again. +# (I don't know why this helps, but sometimes it does. Magic.) + +minimize 1.0e-5 1.0e-7 5000 20000 + +# Run main simulation + +timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs +dump 1 all custom 2500 traj_nvt.lammpstrj id mol type x y z ix iy iz + + +thermo_style custom step temp pe etotal vol epair ebond eangle +thermo 100 # time interval for printing out "thermo" data + + + + +fix fxlan all langevin 300.0 300.0 120 48279 +fix fxnve all nve + +# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB. +# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon. +# Note: The langevin damping parameter "120" corresponds to +# the 0.12ps damping time used in Watson et. al JCP 2011. + +run 1000000 + +write_data system_after_nvt.data + diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README.TXT b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README.TXT new file mode 100644 index 000000000..c3173a1e1 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README.TXT @@ -0,0 +1,17 @@ + +This directory contains an example of a couarse-grained (vaguely protein-like) +heteropolymer consisting of 14 residues, each of which has 2 atoms +(one backbone atom, one residue atom.) + +There are two types of residues, H and P. +The R-atom for the H residue are attracted to eachother. +All other atoms are repulsive. + +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_run.sh b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_run.sh new file mode 100755 index 000000000..1347aebbb --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_run.sh @@ -0,0 +1,20 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.nvt + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_setup.sh b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_setup.sh new file mode 100755 index 000000000..acc5fbbaa --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_visualize.txt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_visualize.txt new file mode 100644 index 000000000..5d97ea56a --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_visualize.txt @@ -0,0 +1,86 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=0.jpg b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=0.jpg new file mode 100644 index 000000000..a57d0309c Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=0.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=1000ps.jpg b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=1000ps.jpg new file mode 100644 index 000000000..c77d7ee9d Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=1000ps.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 000000000..8e82afaec --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,1728 @@ +PSF + + 1 !NTITLE + REMARKS VMD-generated NAMD/X-Plor PSF structure file + + 756 !NATOM + 1 1 1 1 0.000000 13.0000 0 + 2 1 3 3 0.000000 50.0000 0 + 3 1 1 1 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b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead.lt new file mode 100644 index 000000000..8e52f36ba --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead.lt @@ -0,0 +1,128 @@ +# In this example, we define two types of molecules: "H" and "P", +# both containing two atoms, named "CA" and "R". +# +# @R +# | +# @CA +# +# Eventually, we will connect multiple "H" and "P" molecules +# together to form a polymer, as shown below: +# +# @R @R +# | | +# _@CA_ _@CA_ +# ... -.@CA-' `-@CA-' ` ... +# | | +# @R @R +# +# Suppose that the "H" and "P" molecules both use the same +# type of backbone atom ("CA"), but have their own custom "R" +# sidechain atoms with different properties: +# The "R" atoms belonging to "H" molecules are attracted to each other. +# The "R" atoms in "P" molecules are not. +# +# (Note: There is no reason the "H" and "P" molecules in this example need +# to contain the same number of atoms, or the same atom names. +# The point of this example is to illustrate how to share atom types +# and also the difference between local and global atom types.) +# +# By default, all counter variables are local. This means that whenever +# an atom type (or other counter variable) appears inside a molecule +# definition using the normal syntax "@atom:R", that atom type is a local +# property of the the "H" or "P" molecule in which it appears. +# Any properties assigned to the "R" atoms in either molecule are unique +# to that molecule. +# +# However in order to share "CA" atom types, we will override this behavior +# using the "@atom:../CA" syntax instead of "@atom:CA". This will define +# the "CA" atom in the outer (global) environment, and any properties +# (mass, radius, etc...) assigned to the "@atom:../CA" atom apply to +# "CA" atoms in both the the "H" and "P" molecules (and everywhere else). +# +# This might not be a desirable. "CA" is a popular name for carbon +# atoms in different types of molecules. We don't want to prevent other +# molecules from using this atom name. So we enclose the "CA" atom, +# (along with the definitions of the "H" and "P" molecules) within a +# namespace/environment object ("2bead"). This makes the definition +# of "H" and "P" more portable. Later on we can combine "H" and "P" +# molecules with other molecules without worrying whether they contain +# "CA" atoms with different properties. +# +# Note: In this example "2bead" is NOT a molecule. (Because it contains no +# "write("Data Atoms")" section of its own.) "2bead" is simply the +# name of an environment in which other molecules (H,P) are defined. + + + + +2bead { + + write_once("In Init") { + units real + atom_style full + } + + # Define H (the "hydrophobic" residue) + H { + # atom-id mol-id atom-type charge x y z + write("Data Atoms") { + $atom:CA $mol:... @atom:../CA 0.0 0.000 1.0000 0.0000000 + $atom:R $mol:... @atom:R 0.0 0.000 4.4000 0.0000000 + } + + # Old Data Bonds style + # write("Data Bonds") { + # $bond:CR @bond:../sidechain $atom:CA $atom:R + # } + + # New Data Bond List style + write("Data Bond List") { + $bond:CR $atom:CA $atom:R + } + } + + + # Define P (the "polar" residue) + P { + # atom-id mol-id atom-type charge x y z + write("Data Atoms") { + $atom:CA $mol:... @atom:../CA 0.0 0.000 1.0000 0.0000000 + $atom:R $mol:... @atom:R 0.0 0.000 4.4000 0.0000000 + } + + # Old Data Bonds style + # write("Data Bonds") { + # $bond:CR @bond:../sidechain $atom:CA $atom:R + # } + + # New Data Bond List style + write("Data Bond List") { + $bond:CR $atom:CA $atom:R + } + } + + + # (Note: Again, atom types, bond-types, (dihedral-types, any variable, etc) + # can be shared. The ".." in "@atom:../CA" tells moltemplate that + # atom type CA is defined in the parent's environment. (We are + # sharing the CA atom type between both the H and P residues. + # The same is true of the ".." in "@bond:../sidechain". + # + # + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # molecule's id number as it's own. + + + + # There are 3 atom types: the R sidechain (belonging to the H and P residues) + # and the CA sidechain atom (shared by both residues) + + write_once("Data Masses") { + @atom:CA 13.0 + @atom:H/R 50.0 + @atom:P/R 50.0 + } + +} # 2bead + diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_forcefield.lt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_forcefield.lt new file mode 100644 index 000000000..84d82683e --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_forcefield.lt @@ -0,0 +1,126 @@ + +# We define non-bonded and bonded (angular) interactions between atoms +# belonging to "2bead" molecules. +# We define the settings for angles or dihedrals which might be present +# later when we connect multiple "2bead/H" and "2bead/P" molecules together to +# build a polymer. + + +2bead { + + + # LAMMPS supports a large number of force-field styles. We must select + # which ones we need. This information belongs in the "In Init" section. + # (Hybrid styles used for portability. These choices can be overridden later.) + + write_once("In Init") { + # -- Default styles for "2bead" -- + # (Hybrid force fields were not necessary but are used for portability.) + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid charmm + pair_style hybrid lj/cut 11.0 + + # If charges are needed, (assuming biopolymers), try one of: + #dielectric 80.0 + #pair_style hybrid lj/cut/coul/debye 0.1 11.0 + # or (for short distances, below a couple nm) + #pair_style hybrid lj/charmm/coul/charmm/implicit 9.0 11.0 + + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 0.0 + } + + + # OPTIONAL: Enclose these angle settings within the 2bead {...} environment. + # We do this for the same reason we enclosed "H" and "P" in "2bead". + # This does not overwrite the definition of 2bead. Here we are only + # augmenting "2bead" to include the following force field information. + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * ( (sig_ij/r)^12 - (sig_ij/r)^6 ) + # + # Hydrophobic side-chains are attractive (large epsilon parameter). + # Polar side-chains and backbone atoms are not attractive (small epsilon). + # + # i j pairstylename eps sig + # + write_once("In Settings") { + pair_coeff @atom:CA @atom:CA lj/cut 0.10 2.0 + pair_coeff @atom:H/R @atom:H/R lj/cut 2.50 3.6 + pair_coeff @atom:P/R @atom:P/R lj/cut 0.10 3.6 + } + + # (Interactions between different atom types use "arithmetic" mixing rules.) + + write_once("Data Bonds By Type") { + @bond:backbone @atom:CA @atom:CA + @bond:sidechain @atom:CA @atom:*/R + } + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond_coeff bondType bondstylename k r0 + # + + write_once("In Settings") { + bond_coeff @bond:sidechain harmonic 30.0 3.4 + bond_coeff @bond:backbone harmonic 30.0 3.7 + } + + + # Rules for determining 3 and 4-body bonded interactions by type + + # angle-type atomType1 atomType2 atomType3 + + write_once("Data Angles By Type") { + @angle:backbone @atom:CA @atom:CA @atom:CA + @angle:sidechain @atom:CA @atom:CA @atom:*/R + } + + # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 + + write_once("Data Dihedrals By Type") { + @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA + @dihedral:RCCR @atom:*/R @atom:CA @atom:CA @atom:*/R + } + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # The corresponding command is: + # + # angle_coeff angleType anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 30.00 114 + angle_coeff @angle:sidechain harmonic 30.00 123 + } + + + # 4-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Udihedral(phi) = K * (1 + cos(n*phi - d)) + # + # The d parameter is in degrees, K is in kcal/mol/rad^2. + # + # The corresponding command is + # dihedral_coeff dihedralType dihedralstylename K n d w + # "w" is the weight for 1-4 pair interactions, which we set to 0.0 + + write_once("In Settings") { + dihedral_coeff @dihedral:CCCC charmm -0.5 1 -180 0.0 + dihedral_coeff @dihedral:RCCR charmm -1.5 1 -180 0.0 + } # write_once("In Settings") + +} + diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/README.sh new file mode 100755 index 000000000..7604a672c --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/README.sh @@ -0,0 +1,20 @@ +# The version of "2bead.lt" in this directory is defines two types of +# molecules (named "2bead/H" and "2bead/P"). +# +# However, there is another version of this file which is easier to understand. +# I recommend reading that file first. +# It is located at "simplified_version_one_residue/2bead.lt". +# It defines only one type of molecule (named "2bead") +# It is much simpler. + +# ------ + +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + +# run moltemplate + +moltemplate.sh system.lt + +# This will generate various files with names ending in *.in* and *.data. + diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt new file mode 100644 index 000000000..ae125b95f --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt @@ -0,0 +1,50 @@ +import "2bead.lt" + +Peptide { + + # A polymer of alternating "H" and "P" beads: + + res1 = new 2bead/P + res2 = new 2bead/P.rot(180.0, 1,0,0).move(3.2,0,0) + res3 = new 2bead/H.rot( 0.0, 1,0,0).move(6.4,0,0) + res4 = new 2bead/H.rot(180.0, 1,0,0).move(9.6,0,0) + res5 = new 2bead/H.rot( 0.0, 1,0,0).move(12.8,0,0) + res6 = new 2bead/H.rot(180.0, 1,0,0).move(16.0,0,0) + res7 = new 2bead/P.rot( 0.0, 1,0,0).move(19.2,0,0) + res8 = new 2bead/P.rot(180.0, 1,0,0).move(22.4,0,0) + res9 = new 2bead/P.rot( 0.0, 1,0,0).move(25.6,0,0) + res10 = new 2bead/H.rot(180.0, 1,0,0).move(28.8,0,0) + res11 = new 2bead/H.rot( 0.0, 1,0,0).move(32.0,0,0) + res12 = new 2bead/H.rot(180.0, 1,0,0).move(35.2,0,0) + res13 = new 2bead/P.rot( 0.0, 1,0,0).move(38.4,0,0) + res14 = new 2bead/P.rot(180.0, 1,0,0).move(41.6,0,0) + + # Now, link the residues together this way: + write("Data Bond List") { + $bond:backbone1 $atom:res1/CA $atom:res2/CA + $bond:backbone2 $atom:res2/CA $atom:res3/CA + $bond:backbone3 $atom:res3/CA $atom:res4/CA + $bond:backbone4 $atom:res4/CA $atom:res5/CA + $bond:backbone5 $atom:res5/CA $atom:res6/CA + $bond:backbone6 $atom:res6/CA $atom:res7/CA + $bond:backbone7 $atom:res7/CA $atom:res8/CA + $bond:backbone8 $atom:res8/CA $atom:res9/CA + $bond:backbone9 $atom:res9/CA $atom:res10/CA + $bond:backbone10 $atom:res10/CA $atom:res11/CA + $bond:backbone11 $atom:res11/CA $atom:res12/CA + $bond:backbone12 $atom:res12/CA $atom:res13/CA + $bond:backbone13 $atom:res13/CA $atom:res14/CA + } + + create_var { $mol } # <--create a molecule ID number for this peptide + + # This causes res1,res2,res3,...,res14 to share the same molecule counter + # because in the 2bead.lt file, the "..." in "$mol:..." preferentially looks + # for a counter of that type in a parent molecule or earlier ancestor. + +} # Peptide + + + +# Angle, dihedral and improper interactions will be generated +# according to the instructions in "2bead_force_field.lt" diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/system.lt new file mode 100644 index 000000000..2f0d4b5b9 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/system.lt @@ -0,0 +1,26 @@ +import "peptide.lt" +import "2bead_forcefield.lt" + + +# Specify the periodic boundary conditions: +write_once("Data Boundary") { + 0 180.0 xlo xhi + 0 180.0 ylo yhi + 0 180.0 zlo zhi +} + +# Create 27 peptides (=3x3x3) in a rectangular grid + +peptides = new Peptide [3].move(60.0, 0, 0) + [3].move(0, 60.0, 0) + [3].move(0, 0, 60.0) + +# Now (for fun) shift some of the peptides +# in the x direction by a distance of 20.0 +# Suppose we want to move the middle slice +# (which has constant Z). We do that this way: +peptides[1][*][*].move(0,0,20) +# more examples: +peptides[*][1][*].move(20,0,0) +peptides[*][*][1].move(0,20,0) + diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.nvt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.nvt new file mode 100644 index 000000000..eb864e049 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.nvt @@ -0,0 +1,38 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 2.0 +dump 1 all custom 2500 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +fix fxlan all langevin 300.0 300.0 5000.0 48279 +fix fxnve all nve + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 2500 # time interval for printing out "thermo" data + +restart 1000000 restart_nvt + +run 1000000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README.TXT b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README.TXT new file mode 100644 index 000000000..1a077178e --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README.TXT @@ -0,0 +1,36 @@ +This is a very crude attempt to create a polymer melt +consisting of 150 copies of the same polymer. + +THE FORCE FIELD PARAMETERS AND CONFORMATION FOR THIS SYSTEM ARE COMPLETELY WRONG + +The purpose of this example is to demonstrate one way to create a +large number of randomly generated polymers, and to use +an NPT simulation to pack them all into a small box. +(Smaller than their initial outstretched length.) + +Each polymer is a random heteropolymer of length 200 monomers. +This polymer is a polymoer of PVDF and PCTFE monomers +selected randomly in a 1:3 ratio. +Again, this is not a realistic simulation of PVDV or PCTFE polymers, + +Furthermore, even after the simulation is done, the arrangement of the +polymers in the box is not characteristic of a truly random polymer melt. + + +---- A note on size --- + +This is a large system with nearly 200000 atoms. +It takes several minutes to compile this example +and (currently requiring at least 4.0 Gb of memory). +(I'm working on reducing that requirement. -Andrew 2012-9-12) + +----------------------- + +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_run.sh b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_run.sh new file mode 100755 index 000000000..ac21c4c45 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_run.sh @@ -0,0 +1,14 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.nvt diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_setup.sh b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_setup.sh new file mode 100755 index 000000000..acc5fbbaa --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_visualize.txt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_visualize.txt new file mode 100644 index 000000000..019afc144 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/2bead.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/2bead.jpg new file mode 100644 index 000000000..f67da797f Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/2bead.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/3bead.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/3bead.jpg new file mode 100644 index 000000000..15d7b2967 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/3bead.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 000000000..6915e2739 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,277 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 116 !NATOM + 1 1 3 3 0.000000 12.0000 0 + 2 1 4 4 0.000000 17.0000 0 + 3 1 4 4 0.000000 17.0000 0 + 4 1 3 3 0.000000 12.0000 0 + 5 1 4 4 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63 62 64 72 71 73 75 74 76 + 82 81 83 93 92 94 102 101 103 + 109 108 110 + + 47 !NPHI: dihedrals + 38 40 43 46 69 71 74 77 + 1 4 7 9 40 43 46 48 + 67 69 71 74 71 74 77 79 + 35 38 40 43 30 33 35 38 + 28 30 33 35 33 35 38 40 + 57 60 62 65 55 57 60 62 + 4 7 9 11 7 9 11 13 + 13 16 18 20 24 26 28 30 + 62 65 67 69 65 67 69 71 + 81 84 86 88 86 88 90 92 + 92 95 97 99 95 97 99 101 + 108 111 113 115 16 18 20 22 + 18 20 22 24 20 22 24 26 + 22 24 26 28 84 86 88 90 + 9 11 13 16 11 13 16 18 + 26 28 30 33 46 48 50 53 + 53 55 57 60 48 50 53 55 + 60 62 65 67 77 79 81 84 + 79 81 84 86 88 90 92 95 + 90 92 95 97 97 99 101 104 + 104 106 108 111 99 101 104 106 + 106 108 111 113 43 46 48 50 + 50 53 55 57 74 77 79 81 + 101 104 106 108 + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=0ps.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=0ps.jpg new file mode 100644 index 000000000..cc6822e7b Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=0ps.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=1ns.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=1ns.jpg new file mode 100644 index 000000000..efcaa76c0 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=1ns.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/monomers.lt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/monomers.lt new file mode 100644 index 000000000..9a90c172a --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/monomers.lt @@ -0,0 +1,115 @@ + # ---------------------------------------------------------------------- + # -- General comment: -- + # -- The write() and write_once() commands create and append text to -- + # -- files (replacing variables beginning with @ or $ with counters.) -- + # -- File names beginning with "In " or "Data " are special. -- + # -- They will be pasted into the LAMMPS input script and -- + # -- data files which are generated by moltemplate. The syntax -- + # -- of these files is exactly the same as the syntax from the -- + # -- corresponding sections of a LAMMPS input script or data file. -- + # ---------------------------------------------------------------------- + + +MonomerTypes { + + + 2bead { + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:CA $mol:... @atom:CA 0.0 0.000 1.000 0.0000 + $atom:R $mol:... @atom:R 0.0 0.000 4.400 0.0000 + } + + # bond-id bond-type atom-id1 atom-id2 + + write("Data Bonds") { + $bond:CR @bond:../sidechain $atom:CA $atom:R + } + + # atom-type mass + + write_once("Data Masses") { + @atom:CA 12.0 + @atom:R 17.0 + } + + # atom-type atom-type epsilon sigma + + write_once("In Settings") { + pair_coeff @atom:CA @atom:CA 0.10 2.0 + pair_coeff @atom:R @atom:R 0.50 3.0 + } + + } # 2bead + + + 3bead { + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:CA $mol:... @atom:CA 0.0 0.000 1.000 0.000 + $atom:R1 $mol:... @atom:R 0.0 0.000 2.700 2.950 + $atom:R2 $mol:... @atom:R 0.0 0.000 2.700 -2.950 + } + + # bond-id bond-type atom-id1 atom-id2 + + write("Data Bonds") { + $bond:CR1 @bond:../sidechain $atom:CA $atom:R1 + $bond:CR2 @bond:../sidechain $atom:CA $atom:R2 + } + + # atom-type mass + + write_once("Data Masses") { + @atom:CA 12.0 + @atom:R 17.0 + } + + # atom-type atom-type epsilon sigma + + write_once("In Settings") { + pair_coeff @atom:CA @atom:CA 0.10 2.0 + pair_coeff @atom:R @atom:R 0.50 3.0 + } + } # 3bead + + + write_once("In Settings") { + # bond-type k r0 + bond_coeff @bond:sidechain 20.0 3.4 + bond_coeff @bond:bb 20.0 3.4 # "bb" shorthand for "backbone" + } + + # Although there's no need to define angular interactions (because this + # "molecule" only contains two atoms), we define the settings for angles + # or dihedrals which might be present later when we build a polymer. + + write_once("In Settings") { + # angle-type k theta0 + angle_coeff @angle:backbone 10.00 160 + angle_coeff @angle:sidechain 10.00 120 + angle_coeff @angle:RCR 10.00 120 + # dihedral-type K1 K2 K3 K4 + dihedral_coeff @dihedral:backbn 0.10 -0.271016 3.145034 0.0 + } + + # Rules for determining 3 and 4-body bonded interactions by type + + # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 + + write_once("Data Angles By Type") { + @angle:backbone @atom:*/CA @atom:*/CA @atom:*/CA @bond:* @bond:* + @angle:sidechain @atom:*/CA @atom:*/CA @atom:*/R @bond:* @bond:* + @angle:RCR @atom:*/R @atom:*/CA @atom:*/R @bond:* @bond:* + } + + # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3 + + write_once("Data Dihedrals By Type") { + @dihedral:backbn @atom:*/CA @atom:*/CA @atom:*/CA @atom:*/CA * * * + } + +} # MonomerTypes + diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/polymer.lt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/polymer.lt new file mode 100644 index 000000000..9497dcc39 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/polymer.lt @@ -0,0 +1,82 @@ +import "monomers.lt" + +using namespace MonomerTypes + +RandomHeteropolymer { + + # Make a chain of monomers with random composition: + + monomers = new random([2bead,3bead], + [0.6,0.4], + 123456) # <-- optional random seed + [50].rot(180,1,0,0).move(2.95, 0, 0) + + # Now, link the monomers together this way: + + write("Data Bonds") { + $bond:bb1 @bond:MonomerTypes/bb $atom:monomers[0]/CA $atom:monomers[1]/CA + $bond:bb2 @bond:MonomerTypes/bb $atom:monomers[1]/CA $atom:monomers[2]/CA + $bond:bb3 @bond:MonomerTypes/bb $atom:monomers[2]/CA $atom:monomers[3]/CA + $bond:bb4 @bond:MonomerTypes/bb $atom:monomers[3]/CA $atom:monomers[4]/CA + $bond:bb5 @bond:MonomerTypes/bb $atom:monomers[4]/CA $atom:monomers[5]/CA + $bond:bb6 @bond:MonomerTypes/bb $atom:monomers[5]/CA $atom:monomers[6]/CA + $bond:bb7 @bond:MonomerTypes/bb $atom:monomers[6]/CA $atom:monomers[7]/CA + $bond:bb8 @bond:MonomerTypes/bb $atom:monomers[7]/CA $atom:monomers[8]/CA + $bond:bb9 @bond:MonomerTypes/bb $atom:monomers[8]/CA $atom:monomers[9]/CA + $bond:bb10 @bond:MonomerTypes/bb $atom:monomers[9]/CA $atom:monomers[10]/CA + $bond:bb11 @bond:MonomerTypes/bb $atom:monomers[10]/CA $atom:monomers[11]/CA + $bond:bb12 @bond:MonomerTypes/bb $atom:monomers[11]/CA $atom:monomers[12]/CA + $bond:bb13 @bond:MonomerTypes/bb $atom:monomers[12]/CA $atom:monomers[13]/CA + $bond:bb14 @bond:MonomerTypes/bb $atom:monomers[13]/CA $atom:monomers[14]/CA + $bond:bb15 @bond:MonomerTypes/bb $atom:monomers[14]/CA $atom:monomers[15]/CA + $bond:bb16 @bond:MonomerTypes/bb $atom:monomers[15]/CA $atom:monomers[16]/CA + $bond:bb17 @bond:MonomerTypes/bb $atom:monomers[16]/CA $atom:monomers[17]/CA + $bond:bb18 @bond:MonomerTypes/bb $atom:monomers[17]/CA $atom:monomers[18]/CA + $bond:bb19 @bond:MonomerTypes/bb $atom:monomers[18]/CA $atom:monomers[19]/CA + $bond:bb20 @bond:MonomerTypes/bb $atom:monomers[19]/CA $atom:monomers[20]/CA + $bond:bb21 @bond:MonomerTypes/bb $atom:monomers[20]/CA $atom:monomers[21]/CA + $bond:bb22 @bond:MonomerTypes/bb $atom:monomers[21]/CA $atom:monomers[22]/CA + $bond:bb23 @bond:MonomerTypes/bb $atom:monomers[22]/CA $atom:monomers[23]/CA + $bond:bb24 @bond:MonomerTypes/bb $atom:monomers[23]/CA $atom:monomers[24]/CA + $bond:bb25 @bond:MonomerTypes/bb $atom:monomers[24]/CA $atom:monomers[25]/CA + $bond:bb26 @bond:MonomerTypes/bb $atom:monomers[25]/CA $atom:monomers[26]/CA + $bond:bb27 @bond:MonomerTypes/bb $atom:monomers[26]/CA $atom:monomers[27]/CA + $bond:bb28 @bond:MonomerTypes/bb $atom:monomers[27]/CA $atom:monomers[28]/CA + $bond:bb29 @bond:MonomerTypes/bb $atom:monomers[28]/CA $atom:monomers[29]/CA + $bond:bb30 @bond:MonomerTypes/bb $atom:monomers[29]/CA $atom:monomers[30]/CA + $bond:bb31 @bond:MonomerTypes/bb $atom:monomers[30]/CA $atom:monomers[31]/CA + $bond:bb32 @bond:MonomerTypes/bb $atom:monomers[31]/CA $atom:monomers[32]/CA + $bond:bb33 @bond:MonomerTypes/bb $atom:monomers[32]/CA $atom:monomers[33]/CA + $bond:bb34 @bond:MonomerTypes/bb $atom:monomers[33]/CA $atom:monomers[34]/CA + $bond:bb35 @bond:MonomerTypes/bb $atom:monomers[34]/CA $atom:monomers[35]/CA + $bond:bb36 @bond:MonomerTypes/bb $atom:monomers[35]/CA $atom:monomers[36]/CA + $bond:bb37 @bond:MonomerTypes/bb $atom:monomers[36]/CA $atom:monomers[37]/CA + $bond:bb38 @bond:MonomerTypes/bb $atom:monomers[37]/CA $atom:monomers[38]/CA + $bond:bb39 @bond:MonomerTypes/bb $atom:monomers[38]/CA $atom:monomers[39]/CA + $bond:bb40 @bond:MonomerTypes/bb $atom:monomers[39]/CA $atom:monomers[40]/CA + $bond:bb41 @bond:MonomerTypes/bb $atom:monomers[40]/CA $atom:monomers[41]/CA + $bond:bb42 @bond:MonomerTypes/bb $atom:monomers[41]/CA $atom:monomers[42]/CA + $bond:bb43 @bond:MonomerTypes/bb $atom:monomers[42]/CA $atom:monomers[43]/CA + $bond:bb44 @bond:MonomerTypes/bb $atom:monomers[43]/CA $atom:monomers[44]/CA + $bond:bb45 @bond:MonomerTypes/bb $atom:monomers[44]/CA $atom:monomers[45]/CA + $bond:bb46 @bond:MonomerTypes/bb $atom:monomers[45]/CA $atom:monomers[46]/CA + $bond:bb47 @bond:MonomerTypes/bb $atom:monomers[46]/CA $atom:monomers[47]/CA + $bond:bb48 @bond:MonomerTypes/bb $atom:monomers[47]/CA $atom:monomers[48]/CA + $bond:bb49 @bond:MonomerTypes/bb $atom:monomers[48]/CA $atom:monomers[49]/CA + } + + # These lines of moltemplate script above were generated in python: + # for i in range(0,49): + # print(' $bond:bb'+str(i+1)+' @bond:MonomerTypes/bb $atom:monomers[' + # +str(i)+']/CA $atom:monomers['+str(i+1)+']/CA') + + # Finally, create a molecule ID number for this large polymer object + + create_var { $mol } + +} # RandomHeteropolymer + + + +# Angle, dihedral and improper interactions will be generated +# automatically according to the instructions in "monomers.lt" diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/system.lt new file mode 100644 index 000000000..11f2d48fa --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/system.lt @@ -0,0 +1,33 @@ +# LAMMPS supports a large number of force-field styles. We must select +# which ones we need. This information belongs in the "In Init" section (and +# (you can specify it anywhere in your LT files, multiple times if you like). +# If different molecules use different force-field styles, you can use hybrid +# styles. (In this example the molecules share the same pair_style.) + +write_once("In Init") { + units real + atom_style full + bond_style harmonic + angle_style harmonic + dihedral_style opls + pair_style lj/cut 9.0 + # If you have charged molecules immersed in a salty implicit + # solvent, you might try something like this this instead: + # pair_style lj/cut/coul/debye 0.1 9.0 + pair_modify mix arithmetic + dielectric 80.0 + special_bonds lj 0.0 0.0 0.0 +} + + +write_once("Data Boundary") { + 0.0 150.0 xlo xhi + 0.0 150.0 ylo yhi + 0.0 150.0 zlo zhi +} + + +import "polymer.lt" + +polymer = new RandomHeteropolymer + diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/run.in.nvt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/run.in.nvt new file mode 100644 index 000000000..5e08f03cb --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/run.in.nvt @@ -0,0 +1,29 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + +timestep 2.0 +dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 1000 # time interval for printing out "thermo" data + +fix fxlan all langevin 300.0 300.0 120 48279 +fix fxnve all nve + +# Temperature = 500 degrees + +run 500000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_misc/translocation/README.TXT b/tools/moltemplate/examples/CG_misc/translocation/README.TXT new file mode 100644 index 000000000..b9bac96d5 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/README.TXT @@ -0,0 +1,23 @@ + +This example contains a (crude and somewhat simple) example of +the translocation of a (rather short) polymer through a hole in a wall, +surrounded by an explicit LJ solvent. + +(I used a short polymer because a longer polymer would require a larger box. + But this example looked more impressive visually when I used a smaller box.) +---- +Note: You must compile LAMMPS with the optional "RIGID" package installed. To + do this, go to the "src" directory of your lammps installation and type: + make yes-RIGID + make clean-all + make NAME_OF_TARGET #<--("make ubuntu", "make g++", "make linux".) +---- + +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_misc/translocation/README_run.sh b/tools/moltemplate/examples/CG_misc/translocation/README_run.sh new file mode 100755 index 000000000..7078918d5 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/README_run.sh @@ -0,0 +1,28 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.nvt # Run a simulation at constant volume + +#or + +lmp_linux -i run.in.npt # Run a simulation at constant pressure + # (Note: Constant pressure conditions have not been + # well tested. The "run.in.npt" script may fail.) + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.nvt +#or +#mpirun -np 4 lmp_linux -i run.in.npt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_misc/translocation/README_setup.sh b/tools/moltemplate/examples/CG_misc/translocation/README_setup.sh new file mode 100755 index 000000000..acc5fbbaa --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_misc/translocation/README_visualize.txt b/tools/moltemplate/examples/CG_misc/translocation/README_visualize.txt new file mode 100644 index 000000000..019afc144 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_misc/translocation/images/polymer_LR.jpg b/tools/moltemplate/examples/CG_misc/translocation/images/polymer_LR.jpg new file mode 100644 index 000000000..5529fc74b Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/translocation/images/polymer_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/translocation/images/solvent_LR.jpg b/tools/moltemplate/examples/CG_misc/translocation/images/solvent_LR.jpg new file mode 100644 index 000000000..304693e2a Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/translocation/images/solvent_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/translocation/images/walls+solvent+polymer_t=0.jpg b/tools/moltemplate/examples/CG_misc/translocation/images/walls+solvent+polymer_t=0.jpg new file mode 100644 index 000000000..c1dcc4c18 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/translocation/images/walls+solvent+polymer_t=0.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/translocation/images/walls_LR.jpg b/tools/moltemplate/examples/CG_misc/translocation/images/walls_LR.jpg new file mode 100644 index 000000000..319427ae6 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/translocation/images/walls_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/monomer.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/monomer.lt new file mode 100644 index 000000000..a8a35339f --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/monomer.lt @@ -0,0 +1,111 @@ + # ---------------------------------------------------------------------- + # -- General comment: -- + # -- The write() and write_once() commands create and append text to -- + # -- files (replacing variables beginning with @ or $ with counters.) -- + # -- File names beginning with "In " or "Data " are special. -- + # -- They will be pasted into the LAMMPS input script and -- + # -- data files which are generated by moltemplate. The syntax -- + # -- of these files is exactly the same as the syntax from the -- + # -- corresponding sections of a LAMMPS input script or data file. -- + # ---------------------------------------------------------------------- + + +Monomer { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:CA $mol:... @atom:CA 0.0 0.000 0.4000 0.00000 + $atom:R1 $mol:... @atom:R 0.0 0.000 1.000 1.000 + $atom:R2 $mol:... @atom:R 0.0 0.000 1.000 -1.000 + } + + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # parent object's molecule id number as it's own + + + # atom-type mass + + write_once("Data Masses") { + @atom:CA 13.0 + @atom:R 50.0 + } + + # atom-type atom-type epsilon sigma + + write_once("In Settings") { + pair_coeff @atom:CA @atom:CA 0.05 2.0 + pair_coeff @atom:R @atom:R 0.50 2.0 + } + + # bond-id bond-type atom-id1 atom-id2 + + write("Data Bonds") { + $bond:CR1 @bond:sidechain $atom:CA $atom:R1 + $bond:CR2 @bond:sidechain $atom:CA $atom:R2 + } + + write_once("In Settings") { + # bond-type k r0 + bond_coeff @bond:sidechain 30.0 1.2 + bond_coeff @bond:bb 30.0 2.0 # "bb" shorthand for "backbone" + } + + # For a compound molecule consisting of smaller building blocks (such as a + # polymer built from monomers), it is tedious to explicitly list all of the + # angles, dihedrals in the entire molecule. Instead, you can define rules + # for automatically generating all the angular interactions between bonded + # atoms according to their connectivity and the atom/bond type. + # Later, when you connect multiple monomers together to form a polymer, + # appropriate bond-angle forces will be applied to these atoms automatically + # (as well as dihedral and improper forces, if defined). + + # Rules for determining 3 and 4-body bonded interactions by type + + # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 + + write_once("Data Angles By Type") { + @angle:backbone @atom:CA @atom:CA @atom:CA @bond:* @bond:* + @angle:sidechain @atom:CA @atom:CA @atom:R @bond:* @bond:* + @angle:RCR @atom:R @atom:CA @atom:R @bond:* @bond:* + } + + # ("@angle:RCR" defines the angle between the R-C-R atoms within a monomer. + # The other angular interactions are between atoms in neighboring monomers.) + + + # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3 + + write_once("Data Dihedrals By Type") { + @dihedral:backbn @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:* + } + + # Parameters for these new angular interactions must be defined. (I recommend + # putting all force-field parameters (coeffs) in the "In Settings" section.) + + write_once("In Settings") { + # angle-type k theta0 + angle_coeff @angle:backbone 50.00 160 + angle_coeff @angle:sidechain 50.00 120 + angle_coeff @angle:RCR 50.00 120 + # dihedral-type K1 K2 K3 K4 + dihedral_coeff @dihedral:backbn 1.411036 -0.271016 3.145034 0.0 + } + +} # Monomer + + + + + + +# ------------------------------------------------------------------------- +# Heteropolymers: +# +# There is a similar example for heteropolymers which is distributed online +# bundled with the moltemplate software. It is named "2bead_heteropolymer", +# and it demonstrates how to share backbone (CA) atoms, bonds and angles +# (so that you don't have to define them seperately for each type of monomer). +# ------------------------------------------------------------------------- + diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/polymer.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/polymer.lt new file mode 100644 index 000000000..d7ab89dc3 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/polymer.lt @@ -0,0 +1,35 @@ +import "monomer.lt" + +Polymer { + + # Make a chain of monomers + monomers = new Monomer [12].rot(180, 1,0,0).move(2.0, 0, 0) + + + # Now, link the monomers together this way: + write("Data Bonds") { + $bond:bb1 @bond:Monomer/bb $atom:monomers[0]/CA $atom:monomers[1]/CA + $bond:bb2 @bond:Monomer/bb $atom:monomers[1]/CA $atom:monomers[2]/CA + $bond:bb3 @bond:Monomer/bb $atom:monomers[2]/CA $atom:monomers[3]/CA + $bond:bb4 @bond:Monomer/bb $atom:monomers[3]/CA $atom:monomers[4]/CA + $bond:bb5 @bond:Monomer/bb $atom:monomers[4]/CA $atom:monomers[5]/CA + $bond:bb6 @bond:Monomer/bb $atom:monomers[5]/CA $atom:monomers[6]/CA + $bond:bb7 @bond:Monomer/bb $atom:monomers[6]/CA $atom:monomers[7]/CA + $bond:bb8 @bond:Monomer/bb $atom:monomers[7]/CA $atom:monomers[8]/CA + $bond:bb9 @bond:Monomer/bb $atom:monomers[8]/CA $atom:monomers[9]/CA + $bond:bb10 @bond:Monomer/bb $atom:monomers[9]/CA $atom:monomers[10]/CA + $bond:bb11 @bond:Monomer/bb $atom:monomers[10]/CA $atom:monomers[11]/CA + } + + create_var { $mol } # Create a molecule ID number for this polymer + + # This causes monomer[0], monomer[1], ... to share the same molecule counter + # because in the 2bead.lt file, the "..." in "$mol:..." preferentially looks + # for a counter of that type in a parent molecule or earlier ancestor. + +} # Polymer + + + +# Angle, dihedral and improper interactions will be generated +# automatically according to the instructions in "monomer.lt" diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent.lt new file mode 100644 index 000000000..1073a58a1 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent.lt @@ -0,0 +1,23 @@ +###################### SOLVENT ######################### + +import "solvent_single.lt" + +# Fill the simulation box with a solvent. +# In this example, the solvent is made of many +# copies of "MoleculeA" (which has only one atom). + +solvent = new MoleculeA [12].move(3.0,0,0) + [12].move(0,3.0,0) + [12].move(0,0,3.0) + +# To start with a reasonable conformation, it's a good idea to delete the +# solvent where the walls or the polymer is going to be. Here we do it manually: + +delete solvent[*][*][2] # <-- 1st wall will go here +delete solvent[*][*][8] # <-- 2nd wall will go here +delete solvent[6-7][0-8][5-6] # <-- polymer will go here + +# Alternate notation: +# [a:b] notation also works, however the "b" is a strict upper bound... +# ...hence the last line is equivalent to "delete solvent[6:8][0:9][5:7]" +# [a*b] notation also works, and is equivalent to [a-b] diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent_single.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent_single.lt new file mode 100644 index 000000000..8057e3c6f --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent_single.lt @@ -0,0 +1,22 @@ +# The two files "solvent_single.lt" and "wall_single.lt" +# define two very simple molecules containing one atom each. +# Both atoms have a similar size (the have the same sigma parameter). + + +MoleculeA { + + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom:a $mol:. @atom:a 0.0 0.0 0.0 0.0 + } + write_once("Data Masses") { + @atom:a 10.0 + } + write_once("In Settings") { + # i j epsilon sigma cutoff + pair_coeff @atom:a @atom:a 0.60 3.0 7.5 #<--attractive + group groupA type @atom:a #(Atoms of this type belong to the "A" group) + } + +} + diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/system.lt new file mode 100644 index 000000000..90d60d3ba --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/system.lt @@ -0,0 +1,55 @@ + +# LAMMPS supports a large number of force-field styles. We must select +# which ones we need. This information belongs in the "In Init" section (and +# (you can specify it anywhere in your LT files, multiple times if you like). +# If different molecules use different force-field styles, you can use hybrid +# styles. (In this example the molecules share the same pair_style.) + +write_once("In Init") { + units real + atom_style full + bond_style harmonic + angle_style harmonic + dihedral_style opls + pair_style lj/cut 9.0 + # If you have charged molecules immersed in a salty implicit + # solvent, you might try something like this this instead: + # pair_style lj/cut/coul/debye 0.1 9.0 + pair_modify mix arithmetic + dielectric 80.0 + special_bonds lj 0.0 0.0 0.0 +} + + +write_once("Data Boundary") { + 0.0 36.0 xlo xhi + 0.0 36.0 ylo yhi + 0.0 36.0 zlo zhi +} + + +import "solvent.lt" + +import "walls.lt" + +import "polymer.lt" + +polymer = new Polymer +polymer.rot(-90.0, 0,0,1) # rotate it -90 degrees around the Y axis +polymer.move(19.5,22.5,16.5) # move it near the openning of the hole + + + +####################### Notes: ######################### +# +# In this example we deleted solvent and wall molecule objects. +# You can also delete a monomer inside the polymer. To do that use: +# delete polymer/monomers[6] +# You can also delete individual atoms, bonds, angles, dihedrals, & impropers +# from existing molecules. For example to delete an atom in the middle +# of the polymer try this. (Bonds and other interactions will also be removed.) +# delete polymer/monomers[6]/CA +# To delete a bond, try this +# delete polymer/bb6 +# Note: This will not delete the angular interactions. Delete them manually +# Note: In both cases the two molecule fragments will keep the same mol counter. diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/wall_single.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/wall_single.lt new file mode 100644 index 000000000..79275a06b --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/wall_single.lt @@ -0,0 +1,21 @@ +# The two files "solvent_single.lt" and "wall_single.lt" +# define two very simple molecules containing one atom each. +# Both atoms have a similar size (the have the same sigma parameter). + +MoleculeB { + + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom:b $mol:. @atom:b 0.0 0.0 0.0 0.0 + } + write_once("Data Masses") { + @atom:b 10.0 + } + write_once("In Settings") { + # i j epsilon sigma cutoff + pair_coeff @atom:b @atom:b 0.05 3.0 7.5 #<--repulsive (approximately) + group groupB type @atom:b #(Atoms of this type belong to the "B" group) + } + +} + diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/walls.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/walls.lt new file mode 100644 index 000000000..dcccac941 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/walls.lt @@ -0,0 +1,23 @@ +####################### WALLS ########################## + +import "wall_single.lt" + +# Create a wall at position z=6.0 (6.0 = 2*3.0) + +wall1 = new MoleculeB [12].move(3.0, 0, 0) + [12].move(0, 3.0, 0) + +wall1[*][*].move(0,0,6.0) + +# Create a second wall at position z=24.0 (24.0 = 8*3.0) + +wall2 = new MoleculeB [12].move(3.0, 0, 0) + [12].move(0, 3.0, 0) + +wall2[*][*].move(0,0,24.0) + +# Now delete some of the molecules in "wall2" to create a hole. + +delete wall2[6-7][6-9] +delete wall2[5-8][7-8] + diff --git a/tools/moltemplate/examples/CG_misc/translocation/run.in.npt b/tools/moltemplate/examples/CG_misc/translocation/run.in.npt new file mode 100644 index 000000000..328378f06 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/run.in.npt @@ -0,0 +1,70 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 1.0 +dump 1 all custom 500 traj_npt.lammpstrj id mol type x y z ix iy iz + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 500 # time interval for printing out "thermo" data + + +velocity groupB zero angular +velocity groupB zero linear +# (I'm not sure if the two lines above are necessary, but they don't hurt.) + +# Only the groupB atoms are immobile. + +group mobile subtract all groupB + +# ------------------------- NPT --------------------------- + +# Set temp=300K, pressure=500bar, and equilibrate volume only in the z direction + +fix fMoveStuff mobile npt temp 300 300 100 z 500 500 1000.0 dilate mobile + +# ------ QUESTIONABLE (see below): ------ + +fix Ffreezestuff groupB rigid/npt single temp 300 300 100 z 500 500 1000.0 force * off off off torque * off off off dilate mobile + +# -- Alternate npt rigid method -- +# I'm not sure which way is more correct, however +# this also seems to behave in a reasonable-looking way: +#fix Ffreezestuff groupB rigid single force * off off off torque * off off off dilate mobile +# +# The use of either "fix rigid" or "fix rigid/npt" to immobilize +# an object is somewhat controversial. Feel free to omit it. +#(Neither Trung or Steve Plimpton use rigid or rigid/npt for immobilizing +#molecules, but I noticed that at NPT, it does a better job of maintaining +# the correct volume. However "fix rigid" has changed since then (2011), +# so this may no longer be true. Please use this example with caution.) +# ---------------------------------------- + +# IMPORTANT for NPT: You must use "neigh_modify" to turn off calculation of the +# forces between immobilized atoms. +neigh_modify exclude group groupB groupB + +# The next two lines recalculate the temperature +# using only the mobile degrees of freedom: + +compute tempMobile mobile temp +compute pressMobile all pressure tempMobile + +thermo_style custom step c_tempMobile c_pressMobile temp press vol + +fix_modify fMoveStuff temp tempMobile + +run 60000 + +write_restart system_after_npt.rst diff --git a/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt b/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt new file mode 100644 index 000000000..c2e2e8de5 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt @@ -0,0 +1,49 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) + +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz + +thermo_style custom step temp pe etotal vol epair ebond eangle edihed +thermo 500 # time interval for printing out "thermo" data + + +# Optional: Improve efficiency by omitting the calcuation of interactions +# between immobile atoms. (Note: This is not optional under NPT conditions.) +neigh_modify exclude group groupB groupB + +# Only the groupB atoms are immobile. +group mobile subtract all groupB + +# The next two lines recalculate the temperature +# using only the mobile degrees of freedom: + +compute tempMobile mobile temp + +# Integrate the equations of motion: +fix fMoveStuff mobile nvt temp 300.0 300.0 100.0 +fix_modify fMoveStuff temp tempMobile + + +run 100000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README.TXT b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README.TXT new file mode 100644 index 000000000..33eeddda6 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README.TXT @@ -0,0 +1,28 @@ +# -------- REQUIREMENTS: --------- +# 1) This example requires the "MANYBODY" package. +# As of 2012-9, it is included by default, but this may change in the future. +# If lammps complains of a missing pair style enter "make yes-MANYBODY" +# into the shell before compiling lammps. For details see: +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +This is a relatively complex example containing two different types of +molecules, and a hybrid of Lennard-Jones and 3-body SW "pair" styles. + +The cyclododecane molecule uses the +TraPPE force field for hydrocarbon chains. +The parameters for the TraPPE force field are +in a file named "trappe1998.lt" which should be +located in the MOLTEMPLATE_PATH. +(See moltemplate installation instructions.) + +The water solvent is implemented using the 3-body single-particle +coarse-grained "mW" water model: +Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016 + +More detailed instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step 2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_run.sh b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_run.sh new file mode 100755 index 000000000..8220a755c --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_run.sh @@ -0,0 +1,31 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data, system.in.sw +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation are ignored when beginning the simulation at constant volume. +# This can be fixed. Read "run.in.nvt" for equilibration instructions.) + + + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_setup.sh b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_setup.sh new file mode 100755 index 000000000..cb4d90898 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_setup.sh @@ -0,0 +1,25 @@ + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt + + # Here we just want to make sure that the "mW" atom type is assigned to + # number "1". It should be by default, so usually you can leave out + # -a "@atom:/WatMW/mW 1". + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_visualize.txt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_visualize.txt new file mode 100644 index 000000000..019afc144 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=0ps_LR.jpg b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=0ps_LR.jpg new file mode 100644 index 000000000..5123dc7f6 Binary files /dev/null and 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b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane.jpg new file mode 100644 index 000000000..6591b236a Binary files /dev/null and b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane.jpg differ diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane_unrelaxed.jpg b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane_unrelaxed.jpg new file mode 100644 index 000000000..9b4ca06fb Binary files /dev/null and b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane_unrelaxed.jpg differ diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 000000000..97a19f0ff --- /dev/null +++ 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a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/README.sh new file mode 100755 index 000000000..97b9f577d --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/README.sh @@ -0,0 +1,11 @@ +# Use this command to generate the LAMMPS input files: + +moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt + +# The -a argument insures that the "mW" atom type is assigned to "1". +# (This is necessary for the pair_coeff command to work. +# See system.lt for details.) + +# Note: To get rid of the annoying "atom_style unspecified warnings, +# use the "-atomstyle" command line argument, as in: +# moltemplate.sh -atomstyle full -a "@atom:/WatMW/mW 1" system.lt diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/cyclododecane.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/cyclododecane.lt new file mode 100644 index 000000000..ceaa1c69d --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/cyclododecane.lt @@ -0,0 +1,55 @@ +import "trappe1998.lt" + +# The "trappe1998.lt" file is usually located in $MOLTEMPLATE_PATH (and is +# distributed with moltemplate. See the "Installation" section in the manual.) +# It contains definitions of the atoms "CH2", "CH3", and "CH4", as well +# as "saturated" bonds, and the parameters for (bonded/nonbonded) +# interactions between these atoms (all enclosed within the "TraPPE" namespace). + + +Cyclododecane { + + write('Data Atoms') { + $atom:C1 $mol:. @atom:TraPPE/CH2 0.0 0.00000 2.94118 0.0 + $atom:C2 $mol:. @atom:TraPPE/CH2 0.0 0.00000 2.54714 1.47059 + $atom:C3 $mol:. @atom:TraPPE/CH2 0.0 0.00000 1.47059 2.54714 + $atom:C4 $mol:. @atom:TraPPE/CH2 0.0 0.00000 0.0 2.94118 + $atom:C5 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -1.47059 2.54714 + $atom:C6 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -2.54714 1.47059 + $atom:C7 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -2.94118 0.0 + $atom:C8 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -2.54714 -1.47059 + $atom:C9 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -1.47059 -2.54714 + $atom:C10 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -0.0 -2.94118 + $atom:C11 $mol:. @atom:TraPPE/CH2 0.0 0.00000 1.47059 -2.54714 + $atom:C12 $mol:. @atom:TraPPE/CH2 0.0 0.00000 2.54714 -1.47059 + } + + # The "." in "$mol:." refers to the current object's molecule ID, + # and "@atom:TraPPE/CH2" refers to the "CH2" atom-type defined in TraPPE + + write('Data Bonds') { + $bond:bond1 @bond:TraPPE/saturated $atom:C1 $atom:C2 + $bond:bond2 @bond:TraPPE/saturated $atom:C2 $atom:C3 + $bond:bond3 @bond:TraPPE/saturated $atom:C3 $atom:C4 + $bond:bond4 @bond:TraPPE/saturated $atom:C4 $atom:C5 + $bond:bond5 @bond:TraPPE/saturated $atom:C5 $atom:C6 + $bond:bond6 @bond:TraPPE/saturated $atom:C6 $atom:C7 + $bond:bond7 @bond:TraPPE/saturated $atom:C7 $atom:C8 + $bond:bond8 @bond:TraPPE/saturated $atom:C8 $atom:C9 + $bond:bond9 @bond:TraPPE/saturated $atom:C9 $atom:C10 + $bond:bond10 @bond:TraPPE/saturated $atom:C10 $atom:C11 + $bond:bond11 @bond:TraPPE/saturated $atom:C11 $atom:C12 + $bond:bond12 @bond:TraPPE/saturated $atom:C12 $atom:C1 + } + +} # Cyclododecane + + +# coordinates in the "Data Atoms" section generated by this python code: +# from math import * +# bond_length=1.54 +# N=12 +# R=(N*bond_length)/(2*pi) +# for i in range(0,N): +# print('$atom:C'+str(i+1)+' $mol:... @atom:TraPPE/CH2 0.0 0.00000 '+ +# str(round(R*cos(i*2*pi/N),5))+' '+str(round(R*sin(i*2*pi/N),5))) diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/system.lt new file mode 100644 index 000000000..4a7063491 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/system.lt @@ -0,0 +1,62 @@ +# This is a relatively complex example containing two different types of +# molecules, and a hybrid of Lennard-Jones and 3-body SW "pair" styles. + +import "watmw.lt" +import "cyclododecane.lt" + +write_once("Data Boundary") { + 0.000000 48.000 xlo xhi + 0.000000 48.000 ylo yhi + 0.000000 48.000 zlo zhi +} + +wat = new WatMW [12].move(0, 0, 4.0) + [12].move(0, 4.0, 0) + [12].move(4.0, 0, 0) + +cyclododecane = new Cyclododecane [4].move(0, 0, 12.0) + [4].move(0, 12.0, 0) + [4].move(12.0, 0, 0) + +# (Move them by (6.0,6.0,6.0) to avoid overlap with the water.) +cyclododecane[*][*][*].move(6.0,6.0,6.0) + +write_once("In Init") { + # -- Tell LAMMPS we want to use two different pair styles + # -- (This overrides earlier settings.) + pair_style hybrid sw lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 +} + + +write_once("In Settings") { + # -- Now indicate which atom type(s) are simulated using the "sw" pair style + # -- In this case only one of the atom types is used (the mW water "atom"). + + pair_coeff * * sw system.in.sw mW NULL NULL NULL + + # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so + # -- the atoms are identified by order in the list, not by name. (The "mW" + # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) + # -- This command says that the first atom type corresponds to the "mW" + # -- atom in system.in.sw, and to ignore the remaining three atom types + # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. + # -- We don't want to use the "sw" force field for interactions involving + # -- these atom types, so we put "NULL" there.) + # -- Note: For this to work, you should probably run moltemplate this way: + # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt + # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom) +} + + + +# -- Somewhere we must eventually define interactions +# -- between atoms from different molecule types + +write_once("In Settings") { + pair_coeff @atom:WatMW/mW @atom:TraPPE/CH2 lj/charmm/coul/charmm 0.11914784667210733 3.558 + pair_coeff @atom:WatMW/mW @atom:TraPPE/CH3 lj/charmm/coul/charmm 0.17390830404497651 3.458 + pair_coeff @atom:WatMW/mW @atom:TraPPE/CH4 lj/charmm/coul/charmm 0.21371654257637612 3.448 +} + + + diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/trappe1998.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/trappe1998.lt new file mode 100644 index 000000000..9bcc80cb1 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/trappe1998.lt @@ -0,0 +1,50 @@ +# This file stores complete LAMMPS data for the TraPPE model of saturated +# hydrocarbon chains. In this "united-atom" model, each methyl group is +# represented by a single atom. Forces between "atoms" are taken from the +# TraPPE force-field. (J Phys Chem B, 1998, volume 102, pp.2569-2577) + +TraPPE { + + write_once("In Init") { + # -- Default styles for "TraPPE" -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid opls + improper_style none + pair_style hybrid lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:CH2 14.1707 + @atom:CH3 15.2507 + @atom:CH4 16.3307 + } + + write_once("Data Angles By Type") { + @angle:backbone @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated + } + + write_once("Data Dihedrals By Type") { + @dihedral:backbone @atom:CH? @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated @bond:saturated + } + + write_once("In Settings") { + pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95 + pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75 + pair_coeff @atom:CH4 @atom:CH4 lj/charmm/coul/charmm 0.294106636 3.73 + bond_coeff @bond:saturated harmonic 120.0 1.54 + angle_coeff @angle:backbone harmonic 62.0022 114 + dihedral_coeff @dihedral:backbone opls 1.411036 -0.271016 3.145034 0.0 + } + + write_once("In Settings") { + group TraPPE type @atom:CH2 @atom:CH3 @atom:CH4 + } + +} # class TraPPE + diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/version_more_comments/system.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/version_more_comments/system.lt new file mode 100644 index 000000000..34bdfead7 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/version_more_comments/system.lt @@ -0,0 +1,80 @@ +# This is a relatively complex example containing two different types of +# molecules, and a hybrid of Lennard-Jones and 3-body SW "pair" styles. + +import "watmw.lt" +import "cyclododecane.lt" + +write_once("Data Boundary") { + 0.000000 48.000 xlo xhi + 0.000000 48.000 ylo yhi + 0.000000 48.000 zlo zhi +} + +wat = new WatMW [12].move(0, 0, 4.0) + [12].move(0, 4.0, 0) + [12].move(4.0, 0, 0) + +cyclododecane = new Cyclododecane [4].move(0, 0, 12.0) + [4].move(0, 12.0, 0) + [4].move(12.0, 0, 0) + +# (Move them by (6.0,6.0,6.0) to avoid overlap with the water.) +cyclododecane[*][*][*].move(6.0,6.0,6.0) + +write_once("In Init") { + # -- Tell LAMMPS we want to use two different pair styles + # -- (This overrides earlier settings.) + pair_style hybrid sw lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 +} + + + +write_once("In Settings") { + # -- Now indicate which atom type(s) are simulated using the "sw" pair style + # -- In this case only one of the atom types is used (the mW water "atom"). + + pair_coeff * * sw system.in.sw mW NULL NULL NULL + + # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so + # -- the atoms are identified by order in the list, not by name. (The "mW" + # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) + # -- This command says that the first atom type corresponds to the "mW" + # -- atom in system.in.sw, and to ignore the remaining three atom types + # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. + # -- We don't want to use the "sw" force field for interactions involving + # -- these atom types, so we put "NULL" there.) + # + # For this to work, the first atom type (assigned to "1") + # must refer to the "mW" atom type (defined in watmw.lt). + # (This is why we included "watmw.lt" first, to insure that the + # atom counters in WatMW are assinged first, starting with 1.) + # Alternately we can further insure that this happens, it's + # a good idea to run moltemplate.sh using the "-a" argument: + # moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt + # This assigns the atom type named @atom:/WatMW/mW to 1 +} + + + + +# -- Somewhere we must eventually define interactions +# -- between atoms from different molecule types +# -- Now define interactions between DIFFERENT molecules +# Note: In the SPC/E model, the epsilon,sigma parameters for water is 0.1553 +# 3.166. As a crude guess, I chose the LJ parameters for the interaction +# between water & the CH2,CH3,CH4 atoms using Lorentz-Berthelot mixing rules + +write_once("In Settings") { + pair_coeff @atom:WatMW/mW @atom:TraPPE/CH2 lj/charmm/coul/charmm 0.11914784667210733 3.558 + pair_coeff @atom:WatMW/mW @atom:TraPPE/CH3 lj/charmm/coul/charmm 0.17390830404497651 3.458 + pair_coeff @atom:WatMW/mW @atom:TraPPE/CH4 lj/charmm/coul/charmm 0.21371654257637612 3.448 +} + + + + + + + + + diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/watmw.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/watmw.lt new file mode 100644 index 000000000..c7aaecebb --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/watmw.lt @@ -0,0 +1,54 @@ +# This file stores LAMMPS data for the "mW" water model. +# (Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016) +# +# In this model, each water molecule is represented by a single "mW" particle. +# These particles interact with their neighbors via 3-body Stillinger-Weber +# forces whose parameters are tuned to mimic directional hydrogen-bonding +# in liquid water (as well as hexagonal ice, type II ice, and +# low-density super-cooled liquid/amorphous water phases). + +WatMW { + write("Data Atoms") { + $atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:mW 18.02 + } + + write_once("system.in.sw") { + mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.333333333 7.049556277 0.602224558 4 0 0 + } + + write_once("In Init") { + # -- Default styles for "WatMW" -- + units real + pair_style sw + } + + write_once("In Settings") { + # --Now indicate which atom type(s) are simulated using the "sw" pair style + # -- In this case only one of the atom types is used (the mW water "atom"). + + pair_coeff * * sw system.in.sw mW NULL NULL NULL + + # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so + # -- the atoms are identified by order in the list, not by name. (The "mW" + # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) + # -- This command says that the first atom type corresponds to the "mW" + # -- atom in system.in.sw, and to ignore the remaining three atom types + # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. + # -- We don't want to use the "sw" force field for interactions involving + # -- these atom types, so we put "NULL" there.) + # -- Note: For this to work, you should probably run moltemplate this way: + # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt + # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom) + } + + # -- optional -- + + write_once("In Settings") { + group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group) + } + +} # WatMW diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt new file mode 100644 index 000000000..544daee70 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt @@ -0,0 +1,61 @@ +# run.in.npt +# +# -- Usage -- +# +# lmp_linux -i run.in.npt +# (assuming lmp_linux is the name of your lammps binary) +# +# -- Prerequisite Input Files: -- +# systen.data, system.in.init, system.in.settings, system.in.sw +# +# You can generate these files with this command: +# moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt +# --------------------------------- + +# ----- Init Section ----- + + +include system.in.init + + +# ----- Atom Definition Section ----- + + +read_data system.data + + +# ----- Settings Section ----- + + +include system.in.settings + + +# ----- Run Section ----- + + + +# -- minimization protocol -- + +# Note: The minimization step is not necessary in this example. However +# in general, it's always a good idea to minimize the system beforehand. + +minimize 1.0e-5 1.0e-7 100000 400000 + + +# -- simulation protocol -- + + +timestep 2.0 # <- This can be increased to 5.0 or 10.0 for bulk water +dump 1 all custom 500 traj_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 500 # time interval for printing out "thermo" data + +run 200000 + +write_data system_after_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also.) diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt new file mode 100644 index 000000000..66334249b --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt @@ -0,0 +1,81 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# run.in.nvt +# +# -- Usage -- +# +# lmp_g++ -i run.in.nvt +# (assuming lmp_g++ is the name of your lammps binary) +# +# -- Prerequisite Input Files: -- +# systen.data, system.in.init, system.in.settings, system.in.sw +# system_after_npt.data +# +# You can generate these files using this procedure +# +# moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt +# +# lmp_linux -i run.in.npt + +# --------------------------------- + + +# -- init section -- + + +include system.in.init + + + +# -- atom definition section -- + + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + + +# -- settings section -- + + +include system.in.settings + + +# -- run section -- + + +timestep 2.0 +dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz +dump 2 TraPPE custom 1000 traj_alkane_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 + +# The following commands are useful if you want to calculate the distribution +# of alkane-chain radius-of-gyration at a given temperature & pressure. +#compute cRg TraPPE gyration +#variable vRg equal c_cRg +#compute cPE all pe +#variable vPE equal c_cPE +#fix FprintPE all print 1000 "${vPE}" file U.dat +#fix FprintRg all print 1000 "${vRg}" file Rg.dat + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 1000 # time interval for printing out "thermo" data +#thermo_modify flush yes + +restart 100000 restart_nvt + +run 1000000 + +write_data system_after_nvt.data + + diff --git a/tools/moltemplate/examples/README.TXT b/tools/moltemplate/examples/README.TXT new file mode 100644 index 000000000..0ecddbbbd --- /dev/null +++ b/tools/moltemplate/examples/README.TXT @@ -0,0 +1,24 @@ +These are examples for the "moltemplate" molecule builder for LAMMPS. +http://www.moltemplate.org + +Each directory contains one or more examples. + +Each example directory contains: + + images/ This folder has pictures of the molecules in the system + moltemplate_files/ This folder contains LT files and other auxiliary files + README_setup.sh Instructions for how to use moltemplate (executable) + README_visualize.txt Instructions for viewing in DATA/DUMP files in VMD + + ...and one or more LAMMPS input scripts with names like + + run.in.min + run.in.npt + run.in.nvt + +You can run these scripts using + lmp_linux -i run.in.npt +(The name of your lammps binary, "lmp_linux" in this example, may vary. + Sometimes, these scripts must be run in a certain order. For example + it may be necessary to run run.in.min to minimize the system before + you can run the other scripts. These files have not been optimized.) diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/WARNING.TXT b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/WARNING.TXT new file mode 100644 index 000000000..bafcbca1f --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/WARNING.TXT @@ -0,0 +1,72 @@ +# -------- WARNING: -------- + +This directory contains some examples of all-atom simulations using the GAFF +force field, prepared using moltemplate. + +This software is experimental, and the force-fields and equilbration protocols +have not been tested carefully by me. There is no gaurantee that simulations +prepared using moltemplate will reproduce the behavior of AmberTools/AMBER. + +# -------- REQUEST FOR HELP: -------- + +If you notice a problem with these examples, please report it. +Peer-review is the only way to improve this software (or any software). +Other suggestions are also welcome! + +(Contact jewett.aij@gmail.com, 2013-12-01) + + +--- Charge --- + +This software does not assign charges to each atom. +(AmberTools can do this.) + +For the purpose of demonstration, in the hydrocarbon examples located here, +I am simply neglecting the partial charge of the carbon and hydrogen atoms. +This approach is unlikely to be appropriate in most practical applications. + + +--- Long-range electrostatics --- + +Furthermore long-range electrostatics (kspace_style pppm) are usually disabled +by default. (Examples containing TIP3P water are an exception to this.) +To enable long-range coulombics, make these modifications to the +"system.in.init" and "system.in.settings" files AFTER running moltemplate: +(enter these commands into the bash shell) + +echo "kspace_style pppm 0.0001" >> system.in.init +echo "pair_style hybrid lj/charmm/coul/long 9.0 10.0" >> system.in.init +sed -i 's/lj\/charmm\/coul\/charmm/lj\/charmm\/coul\/long/g' system.in.settings + + +--- Improper angles --- + +I am also uncertain whether the improper angle interactions generated by +moltemplate are equivalent to those generated by AmberTools. (I think they are, +but I am worried that I might have listed the atom types in the wrong order.) + + +--- Bloated lammps input scripts --- +--- -> slow simulations ? --- + +As of 2013-12-01, LAMMPS input scripts prepared using moltemplate using the +"gaff.lt" file contain the entire contents of the GAFF force-field, +even if your simulation uses only a few of the atom types in GAFF. + + Details: +Moltemplate creates a file usually named "system.in.settings" containing all +of the GAFF information. It is usually about 700kB large. This file is read +by LAMMPS. This means that every interaction in GAFF is loaded +into LAMMPS (for all ~72 atom types). +This is true even if you only use a tiny subset of the atom types and bonded +interactions defined in GAFF. Hopefully allocating the memory needed to store +this extra information will not slow down your simulations noticably. + +However, in case it does, the "waterTIP3P+isobutane/README_setup.sh" +contains detailed instructions how to strip this kind of junk from +the "system.in.settings" file. + +(In the future I may modify moltemplate to do this automatically, +however I may not remember to remove this warning from this file. +Hopefully this issue will be fixed by the time you use moltemplate.) + diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README.TXT b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README.TXT new file mode 100644 index 000000000..64ec594c6 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README.TXT @@ -0,0 +1,44 @@ +This example is a simple simulation of 288 hexadecane molecules in a box at +room temperature and atmospheric pressure. Please read the WARNING.TXT file. + +-------- REQUIREMENTS: --------- +This example requires building LAMMPS with the "USER-MISC" package. +(because it uses dihedral_style fourier) +To do this, type "make yes-user-misc" before compiling LAMMPS. +http://lammps.sandia.gov/doc/Section_start.html#start_3 + +More detailed instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files: + +step 1) to setup the LAMMPS input files, run this file: +README_setup.sh + + (Currently there is a bug which makes this step slow. + I'll fix it later -Andrew 2013-10-15.) + +step 2) to run LAMMPS, follow the instructions in this file: +README_run.sh + +------------ NOTE: There are two versions of this example. ---------------- + +Both examples use the same force-field parameters. + +1) +In this version, the force-field parameters are loaded from the "gaff.lt" file +(located in the "common" subdirectory). +This frees the user from the drudgery of manually specifying all of these +force-field details for every molecule. (However, the user must be careful +to choose @atom-type names which match AMBER GAFF conventions, +such as the "c3" and "h1" atoms, in this example.) + +2) +Alternately, there is another "hexadecane" example in the "all_atom_examples" +directory. In that example, force-field parameters are loaded from a file +named "alkanes.lt" (instead of "gaff.lt"). The "alkanes.lt" file contains +only the excerpts from "gaff.lt" which are relevant to the hydrocarbon +molcules used in that example. ("gaff.lt" contains parameters for most +small organic molecules, not just hydrocarbons.) +In this way, by editing "alkanes.lt", the user can manually control all of the +force-field details in the simulation. (Without feeling as though they are +relying on some kind of mysterious "black box" to do it for them.) + diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_run.sh b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_run.sh new file mode 100755 index 000000000..8b01ab92d --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_run.sh @@ -0,0 +1,39 @@ +# --- Running LAMMPS --- +# -------- REQUIREMENTS: --------- +# 1) This example requires building LAMMPS with the "USER-MISC" package. +# (because it makes use of "gaff.lt" which uses dihedral_style fourier) +# To do this, type "make yes-user-misc" before compiling LAMMPS. +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# -------- PREREQUISITES: -------- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation might be ignored when beginning the simulation at constant +# volume. (This is because restart files in LAMMPS don't always work, +# and I was spending a lot of time trying to convince people it was a +# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) +# Read the "run.in.nvt" file to find out how to use the "read_restart" +# command to load the results of the pressure-equilibration simulation, +# before beginning a constant-volume run. + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_setup.sh new file mode 100755 index 000000000..3b7fb0990 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_setup.sh @@ -0,0 +1,74 @@ +# -------- REQUIREMENTS: --------- +# You must define your MOLTEMPLATE_PATH environment variable +# and set it to the "common" subdirectory of your moltemplate distribution. +# (See the "Installation" section in the moltemplate manual.) + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + #cp -f system.data system.in* ../ + + + # --------- OPTIONAL STEPS FOR STRIPPING OUT JUNK --------- + # --------- edit 2013-10-13 --------- + echo "-----------------------------------------------------------------" >&2 + echo "OPTIONAL STEP: PRUNING THE RESULTING MOLTEMPLATE OUTPUT TO" >&2 + echo " INCLUDE ONLY ATOMS AND TYPES WE ARE ACTUALLY USING." >&2 + # Unfortunately, as of 2013-8-28, these files contain a lot of irrelevant + # information (for atom types not present in the current system). + # For now, we can strip this out using ltemplify.py to build a new .lt file. + # THIS IS AN UGLY WORKAROUND. HOPEFULLY IN THE FUTURE, WE CAN SKIP THESE STEPS + + # do this in a temporary_directory + mkdir new_lt_file + cd new_lt_file/ + + # now run ltemplify.py + + ltemplify.py ../system.in.init ../system.in.settings ../system.data > system.lt + rm -rf ../system.data ../system.in* # these old lammps files no longer needed + + # This creates a new .LT file named "system.lt" in the local directory. + + + # The ltemplify.py script also does not copy the boundary dimensions. + # We must do this manually. + echo "write_once(\"Data Boundary\") {" >> system.lt + cat "../output_ttree/Data Boundary" >> system.lt + echo "}" >> system.lt + echo "" >> system.lt + # Now, run moltemplate on this new .LT file. + moltemplate.sh system.lt + # This will create: "system.data" "system.in.init" "system.in.settings." + + + # Move the final DATA and INput scripts to the desired location, + mv -f system.data system.in* ../../ + + # and clean up the mess + rm -rf output_ttree/ + cd .. + rm -rf new_lt_file/ + echo "---------------- DONE PRUNING MOLTEMPLATE OUTPUT ----------------" >&2 + echo "-----------------------------------------------------------------" >&2 + # --------- END OF OPTIONAL STEPS FOR STRIPPING OUT JUNK --------- + + + + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + + + +cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_visualize.txt new file mode 100644 index 000000000..019afc144 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/WARNING.TXT b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/WARNING.TXT new file mode 100644 index 000000000..def26ba76 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/WARNING.TXT @@ -0,0 +1,16 @@ +# -------- WARNING: -------- + +This software is experimental, and the force-fields and equilbration protocols +have not been tested carefully by me. There is no gaurantee that the simulation +will reproduce the behavior of real hexadecane molecules, +(or even of hexadecane molecules simulated using AMBER, which should + be using the same force-field). + +# -------- REQUEST FOR HELP: -------- + +However, if you notice a problem with this example, please report it. +I confess I do not have a lot of experience running all-atom simulations. +Peer-review is the only way to improve this software (or any software). +Other suggestions are also welcome! + +(Contact jewett.aij@gmail.com, 2013-10-16) diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg new file mode 100644 index 000000000..b0d31f884 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg new file mode 100644 index 000000000..f7c13d098 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_LR.jpg b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_LR.jpg new file mode 100644 index 000000000..3ad353dbb Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch2group.lt new file mode 100644 index 000000000..8cbfde6a5 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch2group.lt @@ -0,0 +1,49 @@ + +import "gaff.lt" # <-- defines the "GAFF" force field + + +# The "gaff.lt" file is usually located in $MOLTEMPLATE_PATH (and is +# distributed with moltemplate. See the "Installation" section in the manual.) +# It contains definitions of the atoms "c3", "h1", as well as the force-field +# parameters for bonded and non-bonded interactions between them +# (and many other atoms). + +# The charges for the atoms in this example are all set to zero. +# In a realistic simulation, one must assign (partial) charges to each atom. + + +CH2 inherits GAFF { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c3 0.00 0.00 0.000 0.000 + $atom:H1 $mol:... @atom:h1 0.00 0.00 0.6310438442242609 0.8924307629540046 + $atom:H2 $mol:... @atom:h1 0.00 0.00 0.6310438442242609 -0.8924307629540046 + } + + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # parent object's molecule id number as it's own. + # The CH2 group is part of the Hexadecane molecule. + + # Now specify which pairs of atoms are bonded: + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + } + +} # CH2 + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch3group.lt new file mode 100644 index 000000000..2be688c5f --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch3group.lt @@ -0,0 +1,52 @@ + +import "gaff.lt" # <-- defines the "GAFF" force field + + +# The "gaff.lt" file is usually located in $MOLTEMPLATE_PATH (and is +# distributed with moltemplate. See the "Installation" section in the manual.) +# It contains definitions of the atoms "c3", "h1", as well as the force-field +# parameters for bonded and non-bonded interactions between them +# (and many other atoms). + +# The charges for the atoms in this example are all set to zero. +# In a realistic simulation, one must assign (partial) charges to each atom. + + +CH3 inherits GAFF { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c3 0.00 0.00 0.000 0.000 + $atom:H1 $mol:... @atom:h1 0.00 0.00 0.6310438442242609 0.8924307629540046 + $atom:H2 $mol:... @atom:h1 0.00 0.00 0.6310438442242609 -0.8924307629540046 + $atom:H3 $mol:... @atom:h1 0.00 -0.8924307629540046 -0.6310438442242609 0.00 + } + + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # parent object's molecule id number as it's own. + # The CH3 group is part of the Hexadecane molecule. + + # Now specify which pairs of atoms are bonded: + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + $bond:CH3 $atom:C $atom:H3 + } + +} # CH3 + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 + diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/hexadecane.lt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/hexadecane.lt new file mode 100644 index 000000000..fa4a9ac25 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/hexadecane.lt @@ -0,0 +1,84 @@ +# Define the "CH2" and "CH3" objects: + +import "ch2group.lt" +import "ch3group.lt" + + + +Hexadecane inherits GAFF { + + # Create an array of 16 "CH2" objects + + monomers = new CH2.move(0,0.4431163,0) [16].rot(180,1,0,0).move(1.2533223,0,0) + + # "monomers" is a 1-dimensional array containing 16 copies of the CH2 molecule + # Each copy is rotated 180 degrees and shifted along the x axix. + # (For an explanation, read sections 7.1-7.3 of the moltemplate manual.) + # Notes: + # 1.2533223 = DeltaXc = how far each CH2 group is shifted along the axis + # 0.4431163 = DeltaYc/2 = lateral displacement of carbons along axis + + # ---- Now, modify the ends: --- + # Delete the CH2 groups at the beginning and end, and replace them with CH3. + # (Note: Alternately, instead of deleting the CH2 groups at each end, you + # could modify them by adding an extra hydrogen atom to those carbons.) + + delete monomers[0] + delete monomers[15] + monomer_begin = new CH3 + monomer_end = new CH3 + + # Move the CH3 groups to the correct location at either end of the chain: + + monomer_begin.move(0,0.4431163,0) + monomer_end.move(0,0.4431163,0).rot(180,0,0,1).move(18.7998345,0,0) + + # Note: 18.7998345 = (16-1) * DeltaXc + + + # Now add a list of bonds connecting the carbon atoms together: + + write('Data Bond List') { + $bond:b1 $atom:monomer_begin/C $atom:monomers[1]/C + $bond:b2 $atom:monomers[1]/C $atom:monomers[2]/C + $bond:b3 $atom:monomers[2]/C $atom:monomers[3]/C + $bond:b4 $atom:monomers[3]/C $atom:monomers[4]/C + $bond:b5 $atom:monomers[4]/C $atom:monomers[5]/C + $bond:b6 $atom:monomers[5]/C $atom:monomers[6]/C + $bond:b7 $atom:monomers[6]/C $atom:monomers[7]/C + $bond:b8 $atom:monomers[7]/C $atom:monomers[8]/C + $bond:b9 $atom:monomers[8]/C $atom:monomers[9]/C + $bond:b10 $atom:monomers[9]/C $atom:monomers[10]/C + $bond:b11 $atom:monomers[10]/C $atom:monomers[11]/C + $bond:b12 $atom:monomers[11]/C $atom:monomers[12]/C + $bond:b13 $atom:monomers[12]/C $atom:monomers[13]/C + $bond:b14 $atom:monomers[13]/C $atom:monomers[14]/C + $bond:b15 $atom:monomers[14]/C $atom:monomer_end/C + } + + create_var { $mol } # Define a molecule ID number for this polymer + + # This causes monomer[0], monomer[1], ... to share the same molecule-ID. + # (because in the ch2group.lt file, the "..." in "$mol:..." looks for + # a counter of type "$mol" in a parent molecule or earlier ancestor.) + +} # Hexadecane + + + + + + + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/system.lt new file mode 100644 index 000000000..4e0cfaec6 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/system.lt @@ -0,0 +1,18 @@ +import "hexadecane.lt" # <- defines the "Hexadecane" molecule type. + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 62.4 xlo xhi + 0.0 62.4 ylo yhi + 0.0 62.4 zlo zhi +} + +molecules = new Hexadecane [12].move(0, 0, 5.2) + [12].move(0, 5.2, 0) + [2].move(31.2, 0, 0) + + +# NOTE: The spacing between molecules is large. There should be extra room to +# move during the initial stages of equilibration. However, you will have to +# run the simulation at NPT conditions later to compress the system to a +# more realistic density. diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.npt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.npt new file mode 100644 index 000000000..b1791c955 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.npt @@ -0,0 +1,85 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + +# To avvoid explosions, I have a 4-step equilibraion process (expand, minimize, +# reorient, compress). The system (as defined in the "system.data" file) +# is already expanded. That means there are 3 steps left: + +dump dumpeq1 all custom 50 traj_eq1_min.lammpstrj id mol type x y z ix iy iz +thermo 50 + +# -- Equilibration: part 1: initial minimization -- + +# Note: In general, it's always a good idea to minimize the system at first. + +minimize 1.0e-5 1.0e-7 100000 400000 +undump dumpeq1 + +write_data system_after_eq1_min.data + +# -- Equilibration part 2: reorienting the molecules (NVT) -- + +timestep 1.0 +dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy iz + +# Run the system at high temperature (at constant volume) to reorient the +# the molecules (which would otherwise be pointing in the same direction). + +# To speed it up, I randomize the atomic positions for a few thousand steps +# using fix langevin (and fix nve). Then I switch to fix nvt (Nose-Hoover). +# (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.) + + +fix fxlan all langevin 900.0 900.0 120 48279 +fix fxnve all nve + +run 2000 + +unfix fxlan +unfix fxnve +# Now continue the simulation at high temperature using fix nvt (Nose-Hoover). +fix fxnvt all nvt temp 900.0 900.0 100.0 + +run 5000 +undump dumpeq2 + + +write_data system_after_eq2_reorient.data + +unfix fxnvt + +# -- equilibration part 3: Equilibrating the density (NPT) -- + +# Originally, the simulation box (in "system.data" and "system.lt") was +# unrealistically large. The spacing between the molecules was large also. +# I did this to enable the molecules to move freely and reorient themselves. +# After doing that, we should run the simulation under NPT conditions to +# allow the simulation box to contract to it's natural size. We do that here: +# We begin the simulation at 100 barr (a relatively low pressure), and +# slowly decrease it to 1 barr, maintianing the temperature at 300K. + +dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 300.0 300.0 100.0 iso 100.0 1.0 1000.0 drag 2.0 + +timestep 1.0 +run 30000 + +write_data system_after_eq3_npt.data + diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.nvt new file mode 100644 index 000000000..f8b2d31d0 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.nvt @@ -0,0 +1,42 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_eq3_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 350.0 350.0 500.0 tchain 1 +thermo 100 +#thermo_modify flush yes + +run 50000 + +write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README.TXT b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README.TXT new file mode 100644 index 000000000..4ab833f09 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README.TXT @@ -0,0 +1,42 @@ +This is an example of how to use "canned" force-fields in like GAFF in LAMMPS. +In this example, we specify only the atom names, bond connectivity, +(and coordinates and charge), and use moltemplate to +load the GAFF parameters from an external file (gaff.lt) +(...instead of specifying them explicitly in the molecule definition). + +The simulation consists of a mixture of isobutane and water. +Over time (less than 1 ns), the two molecules phase-separate. + +The GAFF parameters are applied only to the isobutane molecule. +(The water molecule paramters are defined explicitly in common/tip3p_2004.lt) +For this to work, make sure you have defined the MOLTEMPLATE_PATH +environment variable and set it to "common". See manual for more details.) + +# WARNING: THIS IS A PRELIMINARY EXAMPLE WHICH USES AMBER'S GAFF FORCE FIELD. +# THIS FEATURE IS CURRENTLY BEING TESTED (AS OF 2013-8-08). +# THE ABILITY TO DETECT AND ASSIGN GAFF FORCE FIELD PARAMETERS +# MOLECULES ACCORDING TO ATOM TYPE IS AN EXPERIMENTAL FEATURE +# AND CURRENTLY PROBABLY HAS BUGS (IN THE DIHEDRALS AND IMPROPERS). +# +# (In addition, I am embarassed to admit I do not understand +# atom nomenclature, and I am not sure if I am using +# the correct GAFF atom names in the isobutane molecule.) +# PLEASE REPORT BUGS AND/OR SEND CORRECTIONS. -A 2013-8-08 +# +# -------- REQUIREMENTS: --------- +# 1) This example requires building LAMMPS with the "USER-MISC" package. +# (because it makes use of "gaff.lt" which uses dihedral_style fourier) +# To do this, type "make yes-user-misc" before compiling LAMMPS. +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) You must define your MOLTEMPLATE_PATH environment variable +# and set it to the "common" subdirectory of your moltemplate distribution. +# (See the "Installation" section in the moltemplate manual.) + +More detailed instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step 2) +README_run.sh diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_run.sh b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_run.sh new file mode 100755 index 000000000..8b01ab92d --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_run.sh @@ -0,0 +1,39 @@ +# --- Running LAMMPS --- +# -------- REQUIREMENTS: --------- +# 1) This example requires building LAMMPS with the "USER-MISC" package. +# (because it makes use of "gaff.lt" which uses dihedral_style fourier) +# To do this, type "make yes-user-misc" before compiling LAMMPS. +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# -------- PREREQUISITES: -------- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation might be ignored when beginning the simulation at constant +# volume. (This is because restart files in LAMMPS don't always work, +# and I was spending a lot of time trying to convince people it was a +# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) +# Read the "run.in.nvt" file to find out how to use the "read_restart" +# command to load the results of the pressure-equilibration simulation, +# before beginning a constant-volume run. + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_setup.sh new file mode 100755 index 000000000..3c7e07165 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_setup.sh @@ -0,0 +1,116 @@ +# -------- REQUIREMENTS: --------- +# You must define your MOLTEMPLATE_PATH environment variable +# and set it to the "common" subdirectory of your moltemplate distribution. +# (See the "Installation" section in the moltemplate manual.) + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + + # FIX THE PAIR STYLES + # (Sorry, this is messy) + # + # I was forced to change the default pair-style for AMBER-force-fields (GAFF) + # from lj/charmm/coul/long to lj/charmm/coul/charmm. (This is because + # LAMMPS crashes when using lj/charmm/coul/long on a system without any + # charged particles, and users were complaining it was moltemplate's fault. + # I wish LAMMPS would not do this.) + # + # Unfortunately, this means that the "Isobutane" molecule (which uses + # AMBER's GAFF), and the "TIP3P_2004" molecule now use different pair styles. + # + # The cleanest way to fix this is to force the two molecules to use + # the same pair style. + # (Using a hybrid pair_style is not practical because that disables mixing + # rules. This would force us to add a huge list of pair_coeff commands to + # explain how TIP3P_2004 atoms interact with all of the various GAFF atoms.) + + # Add a line to systems.in.init to override the pair_style. + # Change the pair_style to "lj/charmm/coul/long 10.0 10.5 10.5". + + echo "pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.5" >> system.in.init + + # Then use "sed" to replace "lj/charmm/coul/charmm" with "lj/charmm/coul/long" + sed -i 's/lj\/charmm\/coul\/charmm/lj\/charmm\/coul\/long/g' system.in.settings + + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + #cp -f system.data system.in* ../ + + + # --------- OPTIONAL STEPS FOR STRIPPING OUT JUNK --------- + # --------- edit 2013-8-28 --------- + echo "-----------------------------------------------------------------" >&2 + echo "OPTIONAL STEP: PRUNING THE RESULTING MOLTEMPLATE OUTPUT TO" >&2 + echo " INCLUDE ONLY ATOMS AND TYPES WE ARE ACTUALLY USING." >&2 + # Unfortunately, as of 2013-8-28, these files contain a lot of irrelevant + # information (for atom types not present in the current system). + # For now, we can strip this out using ltemplify.py to build a new .lt file. + # THIS IS AN UGLY WORKAROUND. HOPEFULLY IN THE FUTURE, WE CAN SKIP THESE STEPS + + # do this in a temporary_directory + mkdir new_lt_file + cd new_lt_file/ + + # now run ltemplify.py + + ltemplify.py ../system.in.init ../system.in.settings ../system.data > system.lt + rm -rf ../system.data ../system.in* # these old lammps files no longer needed + + # This creates a new .LT file named "system.lt" in the local directory. + # Unfortunately, it may be missing some information because ltemplify.py + # does not understand all the commands present in a LAMMPS input script. + # If you define groups or use constraints, you must define them again. In this + # case, we must add the SHAKE constraint for the "TIP3P_2004" water molecule. + # So we have to remember the original name of the bond types and angle types. + # (For this example, SHAKE is applied to the water molecule, which is defined + # in "tip3p_2004.lt" file in the "common/" directory. Check this file.) + ATOMTYPENUM_ow=`awk '{if ($1 == "@/atom:TIP3P_2004/ow") print $2}' < ../output_ttree/ttree_assignments.txt` + ATOMTYPENUM_hw=`awk '{if ($1 == "@/atom:TIP3P_2004/hw") print $2}' < ../output_ttree/ttree_assignments.txt` + BONDTYPENUM=`awk '{if ($1 == "@/bond:TIP3P_2004/OH") print $2}' < ../output_ttree/ttree_assignments.txt` + ANGLETYPENUM=`awk '{if ($1 == "@/angle:TIP3P_2004/HOH") print $2}' < ../output_ttree/ttree_assignments.txt` + echo "" >> system.lt + echo "write_once(\"In Settings\") {" >> system.lt + echo " group tip3p type @atom:type$ATOMTYPENUM_ow @atom:type$ATOMTYPENUM_hw" >> system.lt + echo " fix fShakeTIP3P tip3p shake 0.0001 10 100 b @bond:type$BONDTYPENUM a @angle:type$ANGLETYPENUM" >> system.lt + echo "}" >> system.lt + echo "" >> system.lt + + # The ltemplify.py script also does not copy the boundary dimensions. + # We must do this manually as well. + echo "write_once(\"Data Boundary\") {" >> system.lt + cat "../output_ttree/Data Boundary" >> system.lt + echo "}" >> system.lt + echo "" >> system.lt + # Now, run moltemplate on this new .LT file. + moltemplate.sh system.lt + # This will create: "system.data" "system.in.init" "system.in.settings." + + # move the final DATA and INput scripts to the desired location, + mv -f system.data system.in* ../../ + + # and clean up the mess + rm -rf output_ttree/ + cd .. + rm -rf new_lt_file/ + echo "---------------- DONE PRUNING MOLTEMPLATE OUTPUT ----------------" >&2 + echo "-----------------------------------------------------------------" >&2 + # --------- END OF OPTIONAL STEPS FOR STRIPPING OUT JUNK --------- + + + + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + + + +cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_visualize.txt new file mode 100644 index 000000000..019afc144 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/isobutane.jpg b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/isobutane.jpg new file mode 100644 index 000000000..8c548fba8 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/isobutane.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=0_LR.jpg b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=0_LR.jpg new file mode 100644 index 000000000..fab496aa2 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=0_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=840ps_LR.jpg b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=840ps_LR.jpg new file mode 100644 index 000000000..aaa4abaf5 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=840ps_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water.jpg b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water.jpg new file mode 100644 index 000000000..9d578b4ef Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/isobutane.lt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/isobutane.lt new file mode 100644 index 000000000..10a75296f --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/isobutane.lt @@ -0,0 +1,51 @@ +import "gaff.lt" + +# The "gaff.lt" file is usually located in $MOLTEMPLATE_PATH (and is +# distributed with moltemplate. See the "Installation" section in the manual.) +# It contains definitions of the atoms "c3", "h1", as well as the bonded +# and non-bonded interactions between them (and many other atoms). + +# Moltemplate is a simple text manipulation tool and can not assign atomic +# charge. So the charges for the atoms in this example are all set to zero. +# In a realistic simulation, one must assign (partial) charges to each atom. + + +Isobutane inherits GAFF { + + + write('Data Atoms') { + $atom:C0 $mol:. @atom:c3 0.0 -0.001 -0.001 -0.439 + $atom:C1 $mol:. @atom:c3 0.0 -1.257 -0.726 0.078 + $atom:C2 $mol:. @atom:c3 0.0 1.258 -0.726 0.072 + $atom:C3 $mol:. @atom:c3 0.0 -0.001 1.453 0.069 + $atom:H0 $mol:. @atom:h1 0.0 -0.003 -0.004 -1.439 + $atom:H11 $mol:. @atom:h1 0.0 -2.075 -0.255 -0.254 + $atom:H12 $mol:. @atom:h1 0.0 -1.256 -0.724 1.078 + $atom:H13 $mol:. @atom:h1 0.0 -1.259 -1.669 -0.253 + $atom:H21 $mol:. @atom:h1 0.0 2.074 -0.255 -0.264 + $atom:H22 $mol:. @atom:h1 0.0 1.258 -1.669 -0.259 + $atom:H23 $mol:. @atom:h1 0.0 1.261 -0.724 1.072 + $atom:H31 $mol:. @atom:h1 0.0 -0.817 1.923 -0.263 + $atom:H32 $mol:. @atom:h1 0.0 0.816 1.923 -0.268 + $atom:H33 $mol:. @atom:h1 0.0 0.003 1.456 1.070 + } + + # The "." in "$mol:." refers to the current object's molecule ID, + + write('Data Bond List') { + $bond:C01 $atom:C0 $atom:C1 + $bond:C02 $atom:C0 $atom:C2 + $bond:C03 $atom:C0 $atom:C3 + $bond:C0H $atom:C0 $atom:H0 + $bond:C1H1 $atom:C1 $atom:H11 + $bond:C1H2 $atom:C1 $atom:H12 + $bond:C1H3 $atom:C1 $atom:H13 + $bond:C2H1 $atom:C2 $atom:H21 + $bond:C2H2 $atom:C2 $atom:H22 + $bond:C2H3 $atom:C2 $atom:H23 + $bond:C3H1 $atom:C3 $atom:H31 + $bond:C3H2 $atom:C3 $atom:H32 + $bond:C3H3 $atom:C3 $atom:H33 + } + +} # Isobutane diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/system.lt new file mode 100644 index 000000000..50c539250 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/system.lt @@ -0,0 +1,32 @@ +import "tip3p_2004.lt" + # <- This defines the TIP3P water molecule. This file is + # located in the "common" directory. You can either copy it + # here, or (preferably), you can define a MOLTEMPLATE_PATH + # environment variable and point it to "common". + # (as explained in the installation section of the manual). + +import "isobutane.lt" # <- defines the "Isobutane" molecule type. + + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 41.50 xlo xhi + 0.0 41.50 ylo yhi + 0.0 41.50 zlo zhi +} + + +# The next command generates a (rather dense) cubic lattice with +# spacing 3.45 Angstroms. (The pressure must be equilibrated later.) + +wat = new TIP3P_2004 [12].move(0.00, 0.00, 3.45) + [12].move(0.00, 3.45, 0.00) + [12].move(3.45, 0.00, 0.00) + +isobutane = new Isobutane [4].move(0, 0, 10.35) + [4].move(0, 10.35, 0) + [4].move(10.35, 0, 0) + +# move the isobutane molecules slightly to reduce overlap with the water +isobutane[*][*][*].move(1.725, 1.725, 1.725) + diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.npt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.npt new file mode 100644 index 000000000..03127c1d6 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.npt @@ -0,0 +1,43 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- + +# Note: The minimization step is not necessary in this example. However +# in general, it's always a good idea to minimize the system beforehand. +# fShakeTIP3P was defined in system.in.settings. It is incompatible with "minimize". +unfix fShakeTIP3P +minimize 1.0e-4 1.0e-6 100000 400000 +# Now read "system.in.settings" in order to redefine fShakeTIP3P again: +include system.in.settings + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 500 traj_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 +thermo 100 +#thermo_modify flush yes + +run 2000 + +write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.nvt new file mode 100644 index 000000000..24dd41da3 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.nvt @@ -0,0 +1,51 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + +# COMMENTING OUT MINIMIZATION STEPS: +# If you are reading the coordinates generated by the NPT run +# then you should not need to minimize the system beforehand. +# -- minimization protocol -- +## ("fix shake" is incompatible with "minimize".) +#unfix fShakeTIP3P +#minimize 1.0e-4 1.0e-6 100000 400000 +## Now read "system.in.settings" in order to redefine fShakeTIP3P again: +#include system.in.settings + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 +thermo 500 +#thermo_modify flush yes + +run 50000 + +write_restart system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README.TXT b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README.TXT new file mode 100644 index 000000000..355fe4283 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README.TXT @@ -0,0 +1,54 @@ +NOTE: This example requires the "Al99.eam.alloy" file. + (It was not included in this directory because if its large size.) + As of 2012-11, I was able to obtain it here: + http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy + Copy it to the directory containing this README file. +------------------------------------------------------------------------ +This example shows an alternative way to setup the +aluminum crystal loading simulation described here: +http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression +by Mark Tschopp and Nathan R. Rhodes +For additional backgroumd information, please consult that web page. + +In this example, I use moltemplate to build a "DATA" file for this system. +(I can't think of a compelling reason to do this for simple simulations like +this. But this approach might be useful if you want to artificially create +unusual structures out of aluminum crystals, or mix them with other molecules. +I created this example in response to a user request.) + + + --- To build the system --- + +Carry out the instructions in README_setup.sh, +to generate the LAMMPS DATA file and input scripts you need: +system.data, system.in.init, system.in.settings. +(The run.in script contains references to these files.) + + + --- To run LAMMPS, try a command like: --- + +lmp_linux -i run.in + + or (if you have mpi installed) + +mpirun -np 4 lmp_linux -i run.in + +This will create an ordinary LAMMPS dump file you can visualize with VMD +traj.lammpstrj (See README_visualize.txt) + +It will also create a number of other files, such as: +dump.comp_0.cfg +dump.comp_500.cfg +dump.comp_20000.cfg +Al_comp_100.def1.txt + +The dump.comp_*.cfg files can be visualized using +AtomEye if you have AtomEye and ImageJ installed. +The procedure for doing this is explained in the original tutorial at: +http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression + +The "Al_comp_100.def1.txt" file is a four-column text file containing: +column 1: v_strain = (lx - v_L0)/v_L0 +column 2: -pxx/10000 (diagonal components of the stress tensor) +column 3: -pyy/10000 +column 4: -pzz/10000 diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_setup.sh new file mode 100755 index 000000000..22eb8c435 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_setup.sh @@ -0,0 +1,29 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -atomstyle full system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # We will also need the "Al99.eam.alloy" file: + #cp -f Al99.eam.alloy ../ + # This file was (can be) downloaded from: + # http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy + + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_visualize.txt new file mode 100644 index 000000000..019afc144 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCell_LR.jpg b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCell_LR.jpg new file mode 100644 index 000000000..bf07914da Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCell_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg new file mode 100644 index 000000000..8650cf5cb Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg new file mode 100644 index 000000000..582cf5fe6 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/README.sh b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/README.sh new file mode 100755 index 000000000..64f350f64 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/README.sh @@ -0,0 +1,22 @@ +# This example shows an alternative way to setup the +# aluminum crystal loading simulation described here: +# http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression +# by Mark Tschopp and Nathan R. Rhodes +# For additional backgroumd information, please consult that web page. +# +# In this example, I use moltemplate to build a "DATA" file for this system. +# (I can't think of a compelling reason to do this for simple simulations like +# this. But this approach might be useful if you want to artificially create +# unusual structures out of aluminum crystals, or mix them with other molecules. +# I created this example in response to a user request.) +# +# Use these commands to generate the LAMMPS input script and data file: + +moltemplate.sh system.lt + +# This will generate system.data, system.in.init, system.in.settings. +# In addition to will need to download "Al99.eam.alloy" file. +# (It was not included in this directory because if its large size.) +# As of 2012-11, I was able to obtain it here: +# http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy + diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/al_cell.lt b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/al_cell.lt new file mode 100644 index 000000000..3054a45e0 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/al_cell.lt @@ -0,0 +1,64 @@ +# "AlCell" defines the 4-atom FCC unit cell +# of Aluminum (with a 4.05 angstrom spacing) + +AlCell { + + # AtomID MolID(IGNORE!) AtomType Charge X Y Z + + write("Data Atoms") { + $atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000 + $atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025 + $atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025 + $atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000 + } + + write_once("In Init") { + units metal + atom_style full # <- Requires each atom has a MolID and Charge. + # This is not necessary. (Why use "full"? + # The "full" atom style is useful if you want to + # mix the aluminum with other molecules later. + # Otherwise, just use "atom_style atomic", and + # and remove the 2nd and 4th columns above.) + pair_style eam/alloy + } + + write_once("In Settings") { + pair_coeff * * Al99.eam.alloy Al + } + + write_once("Data Masses") { + @atom:Al 27.0 + } + +} # AlCell + + + + + +# Here is an alternate way to define AlCell +# using "scale(4.05)" to select the lattice spacing: +# +#FccCell { +# write("Data Atoms") { +# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0 +# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5 +# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5 +# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0 +# } +# write_once("Data Masses") { +# @atom:Al 27.0 +# } +# write_once("In Init") { +# units metal +# atom_style full +# pair_style eam/alloy +# } +# write_once("In Settings") { +# pair_coeff * * Al99.eam.alloy Al +# } +#} +# +#AlCell = FccCell.scale(4.05) +# diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/system.lt new file mode 100644 index 000000000..f813c6f66 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/system.lt @@ -0,0 +1,35 @@ + +import "al_cell.lt" # <- this defines the unit cell for aluminum + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 40.50 xlo xhi + 0.0 40.50 ylo yhi + 0.0 40.50 zlo zhi +} + +# The next command generates an array of 10x10x10 AlCell unit cells with +# spacing 4.05 Angstroms. + +unitcells = new AlCell [10].move(0.00, 0.00, 4.05) + [10].move(0.00, 4.05, 0.00) + [10].move(4.05, 0.00, 0.00) + + + + + + + + + + + + +################################################################ +# The next command is not necessary: +# + create_var { $mol } # <-This forces all of the Al atoms in the crystal +# # to share the same molecule ID number. +# # Molecule ID numbers are not necessary. Ignore this. +# diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/run.in b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/run.in new file mode 100644 index 000000000..677cc60ca --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/run.in @@ -0,0 +1,76 @@ +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- +# +# The run-settings below were stolen from: +# +# http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression + + +compute csym all centro/atom fcc +compute peratom all pe/atom + +# EQUILIBRATION +reset_timestep 0 +timestep 0.001 +velocity all create 300 12345 mom yes rot no +fix 1 all npt temp 300 300 1 iso 0 0 1 drag 1 + +# Set thermo output +thermo 1000 +thermo_style custom step lx ly lz press pxx pyy pzz pe temp + +# Run for at least 10 picosecond (assuming 1 fs timestep) +run 20000 +unfix 1 + +# Store final cell length for strain calculations +variable tmp equal "lx" +variable L0 equal ${tmp} +print "Initial Length, L0: ${L0}" + +###################################### +# DEFORMATION +reset_timestep 0 + +fix 1 all npt temp 300 300 1 y 0 0 1 z 0 0 1 drag 1 +variable srate equal 1.0e10 +variable srate1 equal "-v_srate / 1.0e12" +fix 2 all deform 1 x erate ${srate1} units box remap x + +# Output strain and stress info to file +# for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa] +# p2, p3, p4 are in GPa +variable strain equal "(lx - v_L0)/v_L0" +variable p1 equal "v_strain" +variable p2 equal "-pxx/10000" +variable p3 equal "-pyy/10000" +variable p4 equal "-pzz/10000" +fix def1 all print 100 "${p1} ${p2} ${p3} ${p4}" file Al_comp_100.def1.txt screen no + +# Use cfg for AtomEye +dump dAtomEye all cfg 250 dump.comp_*.cfg id type xs ys zs c_csym c_peratom fx fy fz +dump_modify dAtomEye element Al + +# For users without AtomEye (like me), I decided to create a regular dump file: +dump dCoords all custom 250 traj.lammpstrj id type x y z ix iy iz + +# Display thermo +thermo 1000 +thermo_style custom step v_strain temp v_p2 v_p3 v_p4 ke pe press + +run 20000 + +###################################### +# SIMULATION DONE +print "All done" diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT new file mode 100644 index 000000000..d69f1d6ff --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT @@ -0,0 +1,83 @@ +########################################################### +# Interaction of a carbon nanotube with a pair of "mystery +# molecules" (extracted from the cnat-cnt.data/in files). +########################################################### +# Author: Aysun Itai and Andrew Jewett + +This example uses "ltemplify.py" to create molecule templates out +of two different molecules in a pre-existing LAMMPS IN/DATA file. +Then I show how to use "moltemplate.sh" to make copies of these +molecules and to move and rotate them (creating new LAMMPS IN/DATA files). + + Disclaimer: +The molecules in this example are not physically realistic. +The purpose of this example is to demonstrate ltemplify usage. + + REQUIRED INPUT FILES + +cnad-cnt.data cnad-cnt.in system.lt + + cnad-cnt.data + This is a LAMMPS data file containing the coordinates and the topology + for a system combining the two molecules together. ltemplify will extract + molecules from this file, one at a time. + + cnad-cnt.in + This file contains force-field parameters and old run settings for the system. + (We ignore the run settings in this file.) The force-field parameters in + the "cnad-cnt.in" file are only necessary because we are going to build + a completely new set of simulation input files. (We are not only going to + rotate them and duplicate the molecules.) ltemplify.py will extract the + force field parameters from this file. This approach allows us to combine + these molecules with other types of molecules later on.) + + system.lt + The "system.lt" contains the instructions what we will do with these molecules + after ltemplify.py has converted them into .LT format. In this example + it contains instructions for rotating and copying the two molecules, + (It also defines the periodic boundary conditions.) + + OUTPUT FILES + +cnad.lt +cnt.lt + +These files are referenced in system.lt. +Running moltemplate.sh on system.lt (using "moltemplate.sh system.lt") +creates new LAMMPS data and input files: +system.data, system.in, system.in.init, system.in.settings +(These files are referenced in run.in.nvt.) + +You can run a simulation from the files created by moltemplate using + +lmp_linux -i run.in.nvt + +NOTE: BECAUSE ALL OF THE ORIGINAL FORCE FIELD PARAMETERS WERE INTENTIONALLY + ALTERED, THE SYSTEM WILL MOVE IN A VERY UNREALISTIC WAY WHEN SIMULATED. + (This was done to protect the original source of the files.) + The goal of this example is only to demonstrate how to use + "ltemplify.py" to convert lammps input and data files into + LT format and back again.) + + ----------- + +Instructions: +Run the commands (follow the instructions) in these files: + +step 1) +README_step1_run_ltemplify.sh + +and then + +step 2) +README_step2_run_moltemplate.sh + +step 3) OPTIONAL + +To run a short LAMMPS simulation, you can use the "in.nvt" file, for example: + +$LAMMPS_BINARY -i run.in.nvt + +where "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +(such as lmp_linux, lmp_g++, lmp_mac, lmp_ubuntu, lmp_cygwin, etc...). + ----------- diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step1_run_ltemplify.sh b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step1_run_ltemplify.sh new file mode 100755 index 000000000..4bb42d7ea --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step1_run_ltemplify.sh @@ -0,0 +1,13 @@ +#!/bin/sh + +# Aysun Itai's LAMMPS files contain two molecules: + +# The CNAD molecule has molecule-id 1 + +ltemplify.py -name CNAD -molid "1" cnad-cnt.in cnad-cnt.data > cnad.lt + +# The CNT (carbon nanotube) corresponds to molecule-id 2 +ltemplify.py -name CNT -molid "2" cnad-cnt.in cnad-cnt.data > cnt.lt + +# This will extract both molecules and save them as separate .LT files. +# (We can include these files later when preparing new simulations.) diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step2_run_moltemplate.sh b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step2_run_moltemplate.sh new file mode 100755 index 000000000..c99d4b972 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step2_run_moltemplate.sh @@ -0,0 +1,18 @@ +# --- Running Moltemplate --- +# -- Prerequisites: -- +# The "system.lt" moltemplate file links to other ".lt" files +# files you hopefully have created earlier when you ran "ltemplify.py: +# cnad.lt and cnt.lt +# If not, carry out the instructions in "README_run_ltemplify.sh". + +moltemplate.sh system.lt + +# This will generate various files with names ending in *.in* and *.data. +# These files are the input files directly read by LAMMPS. + +# Optional: +# The "./output_ttree/" directory is full of temporary files generated by +# moltemplate. They can be useful for debugging, but are usually thrown away. + +rm -rf output_ttree/ + diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh new file mode 100755 index 000000000..813c406c0 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh @@ -0,0 +1,16 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" LAMMPS input script links to the input +# scripts and data files you hopefully have created earlier +# with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_run_moltemplate.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps this way: + +lmp_linux -i run.in.nvt + +# NOTE: BECAUSE ALL OF THE ORIGINAL FORCE FIELD PARAMETERS WERE INTENTIONALLY +# REMOVED, THE SYSTEM WILL MOVE IN A VERY UNREALISTIC WAY. diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt new file mode 100644 index 000000000..3b9be3e9c --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt @@ -0,0 +1,50 @@ + + ------- To view the trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + + +Later, to Load a trajectory in VMD: + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it + +----- Wrap the coordinates to the unit cell + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Enter: + + DISCLAIMER: I'M NOT SURE THESE COMMANDS ARE CORRECT. + LOOKUP "pbctools" FOR DETAILS. + + pbc wrap -compound res -all + pbc box + +3) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data new file mode 100644 index 000000000..1f18ff4ae --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data @@ -0,0 +1,1157 @@ +Created by Aysun Itai and modified by Andrew Jewett +NOTE: This file has been extensively modified. +Only the bond connectivity and atomic positions are accurate. + + 101 atoms + 134 bonds + 252 angles + 457 dihedrals + 0 impropers + + 16 atom types + 24 bond types + 50 angle types + 78 dihedral types + 0 improper types + + 0 50 xlo xhi + 0 50 ylo yhi + 0 50 zlo zhi + +Masses + + 1 10.0 + 2 10.0 # atom type names often appear + 3 10.0 # in the comments follwing + 4 10.0 # each line in the Masses section + 5 10.0 + 6 10.0 + 7 10.0 + 8 10.0 + 9 10.0 + 10 10.0 + 11 10.0 + 12 10.0 + 13 10.0 + 14 10.0 + 15 10.0 + 16 10.0 + +Atoms + +1 2 1 0.000000 12.345 10.000 4.328 +2 2 1 0.000000 12.031 11.173 5.037 +3 2 1 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9.291 +31 2 1 0.000000 10.000 12.345 10.709 +32 2 1 0.000000 8.827 12.031 11.418 +33 2 1 0.000000 8.827 12.031 8.582 +34 2 1 0.000000 7.969 11.173 9.291 +35 2 1 0.000000 7.969 11.173 10.709 +36 2 1 0.000000 7.655 10.000 11.418 +37 2 1 0.000000 7.655 10.000 8.582 +38 2 1 0.000000 7.969 8.827 9.291 +39 2 1 0.000000 7.969 8.827 10.709 +40 2 1 0.000000 8.827 7.969 11.418 +41 2 1 0.000000 8.827 7.969 8.582 +42 2 1 0.000000 10.000 7.655 9.291 +43 2 1 0.000000 10.000 7.655 10.709 +44 2 1 0.000000 11.173 7.969 11.418 +45 2 1 0.000000 11.173 7.969 8.582 +46 2 1 0.000000 12.031 8.827 9.291 +47 2 1 0.000000 12.031 8.827 10.709 +48 2 1 0.000000 12.345 10.000 11.418 +49 2 1 0.000000 12.345 10.000 12.836 +50 2 1 0.000000 12.031 11.173 13.545 +51 2 1 0.000000 12.031 11.173 14.963 +52 2 1 0.000000 11.173 12.031 15.672 +53 2 1 0.000000 11.173 12.031 12.836 +54 2 1 0.000000 10.000 12.345 13.545 +55 2 1 0.000000 10.000 12.345 14.963 +56 2 1 0.000000 8.827 12.031 15.672 +57 2 1 0.000000 8.827 12.031 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@@ -0,0 +1,49 @@ +#Created by Aysun Itai and modified by Andrew Jewett +# NOTE: This file has been extensively modified. +# Only the bond connectivity and atomic positions are accurate. + +units real + +neigh_modify delay 2 every 1 + +atom_style full +bond_style harmonic +angle_style charmm +dihedral_style charmm +pair_style lj/charmm/coul/charmm 8.0 10.0 +pair_modify mix arithmetic + +read_data cnad-cnt.data + +pair_coeff 1 1 0.02 4.0 +pair_coeff 2 2 0.02 1.0 # atoms will not interact sterically +pair_coeff 3 3 0.02 2.0 # in this version of the file. +pair_coeff 4 4 0.02 2.0 # (All pair forces and atom names removed) +pair_coeff 5 5 0.02 2.0 +pair_coeff 6 6 0.02 3.0 +pair_coeff 7 7 0.02 3.0 +pair_coeff 8 8 0.02 3.0 +pair_coeff 9 9 0.02 4.0 +pair_coeff 10 10 0.02 4.0 +pair_coeff 11 11 0.02 4.0 +pair_coeff 12 12 0.02 4.0 +pair_coeff 13 13 0.02 3.0 +pair_coeff 14 14 0.02 3.0 +pair_coeff 15 15 0.02 3.0 +pair_coeff 16 16 0.02 3.0 + +group cnt type 1 +group cnad type 2-16 + +displace_atoms cnad move 0 -7 0 units box +special_bonds charmm + +velocity all create 0.0 54321 dist uniform + +thermo 1 +thermo_style multi +timestep 0.005 + +dump 1 all atom 10 cnad-cnt.dump + +run 20000 diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnt.lt b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnt.lt new file mode 100644 index 000000000..5f53579d6 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnt.lt @@ -0,0 +1,779 @@ +CNT { + +### LAMMPS commands for initialization +### (These can be overridden later.) + + + write_once("In Init") { + units real + atom_style full + bond_style harmonic + angle_style charmm + dihedral_style charmm + pair_style lj/charmm/coul/charmm 8.0 10.0 + pair_modify mix arithmetic + special_bonds charmm + } + + write_once("In Settings") { + pair_coeff @atom:type1 @atom:type1 0.02 4.0 + } + +### DATA sections + + + write_once("Data Masses") { + @atom:type1 10.0 + } + + write_once("Data Bond Coeffs") { + @bond:type1 2.0 1.4 + } + + write_once("Data Angle Coeffs") { + @angle:type1 0 120.0 0 2.0 + } + + write_once("Data Dihedral Coeffs") { + @dihedral:type1 0.0 2 180 1 + } + + write("Data Atoms") { + $atom:id1 $mol:id2 @atom:type1 0.000000 12.345 10.000 4.328 + $atom:id2 $mol:id2 @atom:type1 0.000000 12.031 11.173 5.037 + $atom:id3 $mol:id2 @atom:type1 0.000000 12.031 11.173 6.455 + $atom:id4 $mol:id2 @atom:type1 0.000000 11.173 12.031 7.164 + $atom:id5 $mol:id2 @atom:type1 0.000000 11.173 12.031 4.328 + $atom:id6 $mol:id2 @atom:type1 0.000000 10.000 12.345 5.037 + $atom:id7 $mol:id2 @atom:type1 0.000000 10.000 12.345 6.455 + $atom:id8 $mol:id2 @atom:type1 0.000000 8.827 12.031 7.164 + $atom:id9 $mol:id2 @atom:type1 0.000000 8.827 12.031 4.328 + $atom:id10 $mol:id2 @atom:type1 0.000000 7.969 11.173 5.037 + $atom:id11 $mol:id2 @atom:type1 0.000000 7.969 11.173 6.455 + $atom:id12 $mol:id2 @atom:type1 0.000000 7.655 10.000 7.164 + $atom:id13 $mol:id2 @atom:type1 0.000000 7.655 10.000 4.328 + $atom:id14 $mol:id2 @atom:type1 0.000000 7.969 8.827 5.037 + $atom:id15 $mol:id2 @atom:type1 0.000000 7.969 8.827 6.455 + $atom:id16 $mol:id2 @atom:type1 0.000000 8.827 7.969 7.164 + $atom:id17 $mol:id2 @atom:type1 0.000000 8.827 7.969 4.328 + $atom:id18 $mol:id2 @atom:type1 0.000000 10.000 7.655 5.037 + $atom:id19 $mol:id2 @atom:type1 0.000000 10.000 7.655 6.455 + $atom:id20 $mol:id2 @atom:type1 0.000000 11.173 7.969 7.164 + $atom:id21 $mol:id2 @atom:type1 0.000000 11.173 7.969 4.328 + $atom:id22 $mol:id2 @atom:type1 0.000000 12.031 8.827 5.037 + $atom:id23 $mol:id2 @atom:type1 0.000000 12.031 8.827 6.455 + $atom:id24 $mol:id2 @atom:type1 0.000000 12.345 10.000 7.164 + $atom:id25 $mol:id2 @atom:type1 0.000000 12.345 10.000 8.582 + $atom:id26 $mol:id2 @atom:type1 0.000000 12.031 11.173 9.291 + $atom:id27 $mol:id2 @atom:type1 0.000000 12.031 11.173 10.709 + $atom:id28 $mol:id2 @atom:type1 0.000000 11.173 12.031 11.418 + $atom:id29 $mol:id2 @atom:type1 0.000000 11.173 12.031 8.582 + $atom:id30 $mol:id2 @atom:type1 0.000000 10.000 12.345 9.291 + $atom:id31 $mol:id2 @atom:type1 0.000000 10.000 12.345 10.709 + $atom:id32 $mol:id2 @atom:type1 0.000000 8.827 12.031 11.418 + $atom:id33 $mol:id2 @atom:type1 0.000000 8.827 12.031 8.582 + $atom:id34 $mol:id2 @atom:type1 0.000000 7.969 11.173 9.291 + $atom:id35 $mol:id2 @atom:type1 0.000000 7.969 11.173 10.709 + $atom:id36 $mol:id2 @atom:type1 0.000000 7.655 10.000 11.418 + $atom:id37 $mol:id2 @atom:type1 0.000000 7.655 10.000 8.582 + $atom:id38 $mol:id2 @atom:type1 0.000000 7.969 8.827 9.291 + $atom:id39 $mol:id2 @atom:type1 0.000000 7.969 8.827 10.709 + $atom:id40 $mol:id2 @atom:type1 0.000000 8.827 7.969 11.418 + $atom:id41 $mol:id2 @atom:type1 0.000000 8.827 7.969 8.582 + $atom:id42 $mol:id2 @atom:type1 0.000000 10.000 7.655 9.291 + $atom:id43 $mol:id2 @atom:type1 0.000000 10.000 7.655 10.709 + $atom:id44 $mol:id2 @atom:type1 0.000000 11.173 7.969 11.418 + $atom:id45 $mol:id2 @atom:type1 0.000000 11.173 7.969 8.582 + $atom:id46 $mol:id2 @atom:type1 0.000000 12.031 8.827 9.291 + $atom:id47 $mol:id2 @atom:type1 0.000000 12.031 8.827 10.709 + $atom:id48 $mol:id2 @atom:type1 0.000000 12.345 10.000 11.418 + $atom:id49 $mol:id2 @atom:type1 0.000000 12.345 10.000 12.836 + $atom:id50 $mol:id2 @atom:type1 0.000000 12.031 11.173 13.545 + $atom:id51 $mol:id2 @atom:type1 0.000000 12.031 11.173 14.963 + $atom:id52 $mol:id2 @atom:type1 0.000000 11.173 12.031 15.672 + $atom:id53 $mol:id2 @atom:type1 0.000000 11.173 12.031 12.836 + $atom:id54 $mol:id2 @atom:type1 0.000000 10.000 12.345 13.545 + $atom:id55 $mol:id2 @atom:type1 0.000000 10.000 12.345 14.963 + $atom:id56 $mol:id2 @atom:type1 0.000000 8.827 12.031 15.672 + $atom:id57 $mol:id2 @atom:type1 0.000000 8.827 12.031 12.836 + $atom:id58 $mol:id2 @atom:type1 0.000000 7.969 11.173 13.545 + $atom:id59 $mol:id2 @atom:type1 0.000000 7.969 11.173 14.963 + $atom:id60 $mol:id2 @atom:type1 0.000000 7.655 10.000 15.672 + $atom:id61 $mol:id2 @atom:type1 0.000000 7.655 10.000 12.836 + $atom:id62 $mol:id2 @atom:type1 0.000000 7.969 8.827 13.545 + $atom:id63 $mol:id2 @atom:type1 0.000000 7.969 8.827 14.963 + $atom:id64 $mol:id2 @atom:type1 0.000000 8.827 7.969 15.672 + $atom:id65 $mol:id2 @atom:type1 0.000000 8.827 7.969 12.836 + $atom:id66 $mol:id2 @atom:type1 0.000000 10.000 7.655 13.545 + $atom:id67 $mol:id2 @atom:type1 0.000000 10.000 7.655 14.963 + $atom:id68 $mol:id2 @atom:type1 0.000000 11.173 7.969 15.672 + $atom:id69 $mol:id2 @atom:type1 0.000000 11.173 7.969 12.836 + $atom:id70 $mol:id2 @atom:type1 0.000000 12.031 8.827 13.545 + $atom:id71 $mol:id2 @atom:type1 0.000000 12.031 8.827 14.963 + $atom:id72 $mol:id2 @atom:type1 0.000000 12.345 10.000 15.672 + } + + write("Data Bonds") { + $bond:id1 @bond:type1 $atom:id1 $atom:id2 + $bond:id2 @bond:type1 $atom:id1 $atom:id22 + $bond:id3 @bond:type1 $atom:id2 $atom:id3 + $bond:id4 @bond:type1 $atom:id2 $atom:id5 + $bond:id5 @bond:type1 $atom:id3 $atom:id24 + $bond:id6 @bond:type1 $atom:id3 $atom:id4 + $bond:id7 @bond:type1 $atom:id4 $atom:id7 + $bond:id8 @bond:type1 $atom:id4 $atom:id29 + $bond:id9 @bond:type1 $atom:id5 $atom:id6 + $bond:id10 @bond:type1 $atom:id6 $atom:id7 + $bond:id11 @bond:type1 $atom:id6 $atom:id9 + $bond:id12 @bond:type1 $atom:id7 $atom:id8 + $bond:id13 @bond:type1 $atom:id8 $atom:id33 + $bond:id14 @bond:type1 $atom:id8 $atom:id11 + $bond:id15 @bond:type1 $atom:id9 $atom:id10 + $bond:id16 @bond:type1 $atom:id10 $atom:id13 + $bond:id17 @bond:type1 $atom:id10 $atom:id11 + $bond:id18 @bond:type1 $atom:id11 $atom:id12 + $bond:id19 @bond:type1 $atom:id12 $atom:id15 + $bond:id20 @bond:type1 $atom:id12 $atom:id37 + $bond:id21 @bond:type1 $atom:id13 $atom:id14 + $bond:id22 @bond:type1 $atom:id14 $atom:id17 + $bond:id23 @bond:type1 $atom:id14 $atom:id15 + $bond:id24 @bond:type1 $atom:id15 $atom:id16 + $bond:id25 @bond:type1 $atom:id16 $atom:id19 + $bond:id26 @bond:type1 $atom:id16 $atom:id41 + $bond:id27 @bond:type1 $atom:id17 $atom:id18 + $bond:id28 @bond:type1 $atom:id18 $atom:id21 + $bond:id29 @bond:type1 $atom:id18 $atom:id19 + $bond:id30 @bond:type1 $atom:id19 $atom:id20 + $bond:id31 @bond:type1 $atom:id20 $atom:id23 + $bond:id32 @bond:type1 $atom:id20 $atom:id45 + $bond:id33 @bond:type1 $atom:id21 $atom:id22 + $bond:id34 @bond:type1 $atom:id22 $atom:id23 + $bond:id35 @bond:type1 $atom:id23 $atom:id24 + $bond:id36 @bond:type1 $atom:id24 $atom:id25 + $bond:id37 @bond:type1 $atom:id25 $atom:id26 + $bond:id38 @bond:type1 $atom:id25 $atom:id46 + $bond:id39 @bond:type1 $atom:id26 $atom:id27 + $bond:id40 @bond:type1 $atom:id26 $atom:id29 + $bond:id41 @bond:type1 $atom:id27 $atom:id48 + $bond:id42 @bond:type1 $atom:id27 $atom:id28 + $bond:id43 @bond:type1 $atom:id28 $atom:id31 + $bond:id44 @bond:type1 $atom:id28 $atom:id53 + $bond:id45 @bond:type1 $atom:id29 $atom:id30 + $bond:id46 @bond:type1 $atom:id30 $atom:id31 + $bond:id47 @bond:type1 $atom:id30 $atom:id33 + $bond:id48 @bond:type1 $atom:id31 $atom:id32 + $bond:id49 @bond:type1 $atom:id32 $atom:id57 + $bond:id50 @bond:type1 $atom:id32 $atom:id35 + $bond:id51 @bond:type1 $atom:id33 $atom:id34 + $bond:id52 @bond:type1 $atom:id34 $atom:id37 + $bond:id53 @bond:type1 $atom:id34 $atom:id35 + $bond:id54 @bond:type1 $atom:id35 $atom:id36 + $bond:id55 @bond:type1 $atom:id36 $atom:id39 + $bond:id56 @bond:type1 $atom:id36 $atom:id61 + $bond:id57 @bond:type1 $atom:id37 $atom:id38 + $bond:id58 @bond:type1 $atom:id38 $atom:id41 + $bond:id59 @bond:type1 $atom:id38 $atom:id39 + $bond:id60 @bond:type1 $atom:id39 $atom:id40 + $bond:id61 @bond:type1 $atom:id40 $atom:id43 + $bond:id62 @bond:type1 $atom:id40 $atom:id65 + $bond:id63 @bond:type1 $atom:id41 $atom:id42 + $bond:id64 @bond:type1 $atom:id42 $atom:id45 + $bond:id65 @bond:type1 $atom:id42 $atom:id43 + $bond:id66 @bond:type1 $atom:id43 $atom:id44 + $bond:id67 @bond:type1 $atom:id44 $atom:id47 + $bond:id68 @bond:type1 $atom:id44 $atom:id69 + $bond:id69 @bond:type1 $atom:id45 $atom:id46 + $bond:id70 @bond:type1 $atom:id46 $atom:id47 + $bond:id71 @bond:type1 $atom:id47 $atom:id48 + $bond:id72 @bond:type1 $atom:id48 $atom:id49 + $bond:id73 @bond:type1 $atom:id49 $atom:id50 + $bond:id74 @bond:type1 $atom:id49 $atom:id70 + $bond:id75 @bond:type1 $atom:id50 $atom:id51 + $bond:id76 @bond:type1 $atom:id50 $atom:id53 + $bond:id77 @bond:type1 $atom:id51 $atom:id72 + $bond:id78 @bond:type1 $atom:id51 $atom:id52 + $bond:id79 @bond:type1 $atom:id52 $atom:id55 + $bond:id80 @bond:type1 $atom:id53 $atom:id54 + $bond:id81 @bond:type1 $atom:id54 $atom:id55 + $bond:id82 @bond:type1 $atom:id54 $atom:id57 + $bond:id83 @bond:type1 $atom:id55 $atom:id56 + $bond:id84 @bond:type1 $atom:id56 $atom:id59 + $bond:id85 @bond:type1 $atom:id57 $atom:id58 + $bond:id86 @bond:type1 $atom:id58 $atom:id61 + $bond:id87 @bond:type1 $atom:id58 $atom:id59 + $bond:id88 @bond:type1 $atom:id59 $atom:id60 + $bond:id89 @bond:type1 $atom:id60 $atom:id63 + $bond:id90 @bond:type1 $atom:id61 $atom:id62 + $bond:id91 @bond:type1 $atom:id62 $atom:id65 + $bond:id92 @bond:type1 $atom:id62 $atom:id63 + $bond:id93 @bond:type1 $atom:id63 $atom:id64 + $bond:id94 @bond:type1 $atom:id64 $atom:id67 + $bond:id95 @bond:type1 $atom:id65 $atom:id66 + $bond:id96 @bond:type1 $atom:id66 $atom:id69 + $bond:id97 @bond:type1 $atom:id66 $atom:id67 + $bond:id98 @bond:type1 $atom:id67 $atom:id68 + $bond:id99 @bond:type1 $atom:id68 $atom:id71 + $bond:id100 @bond:type1 $atom:id69 $atom:id70 + $bond:id101 @bond:type1 $atom:id70 $atom:id71 + $bond:id102 @bond:type1 $atom:id71 $atom:id72 + } + + write("Data Angles") { + $angle:id1 @angle:type1 $atom:id2 $atom:id1 $atom:id22 + $angle:id2 @angle:type1 $atom:id1 $atom:id2 $atom:id3 + $angle:id3 @angle:type1 $atom:id1 $atom:id2 $atom:id5 + $angle:id4 @angle:type1 $atom:id3 $atom:id2 $atom:id5 + $angle:id5 @angle:type1 $atom:id2 $atom:id3 $atom:id24 + $angle:id6 @angle:type1 $atom:id2 $atom:id3 $atom:id4 + $angle:id7 @angle:type1 $atom:id4 $atom:id3 $atom:id24 + $angle:id8 @angle:type1 $atom:id3 $atom:id4 $atom:id7 + $angle:id9 @angle:type1 $atom:id3 $atom:id4 $atom:id29 + $angle:id10 @angle:type1 $atom:id7 $atom:id4 $atom:id29 + $angle:id11 @angle:type1 $atom:id2 $atom:id5 $atom:id6 + $angle:id12 @angle:type1 $atom:id5 $atom:id6 $atom:id7 + $angle:id13 @angle:type1 $atom:id5 $atom:id6 $atom:id9 + $angle:id14 @angle:type1 $atom:id7 $atom:id6 $atom:id9 + $angle:id15 @angle:type1 $atom:id4 $atom:id7 $atom:id6 + $angle:id16 @angle:type1 $atom:id4 $atom:id7 $atom:id8 + $angle:id17 @angle:type1 $atom:id6 $atom:id7 $atom:id8 + $angle:id18 @angle:type1 $atom:id7 $atom:id8 $atom:id33 + $angle:id19 @angle:type1 $atom:id7 $atom:id8 $atom:id11 + $angle:id20 @angle:type1 $atom:id11 $atom:id8 $atom:id33 + $angle:id21 @angle:type1 $atom:id6 $atom:id9 $atom:id10 + $angle:id22 @angle:type1 $atom:id9 $atom:id10 $atom:id13 + $angle:id23 @angle:type1 $atom:id9 $atom:id10 $atom:id11 + $angle:id24 @angle:type1 $atom:id11 $atom:id10 $atom:id13 + $angle:id25 @angle:type1 $atom:id8 $atom:id11 $atom:id10 + $angle:id26 @angle:type1 $atom:id8 $atom:id11 $atom:id12 + $angle:id27 @angle:type1 $atom:id10 $atom:id11 $atom:id12 + $angle:id28 @angle:type1 $atom:id11 $atom:id12 $atom:id15 + $angle:id29 @angle:type1 $atom:id11 $atom:id12 $atom:id37 + $angle:id30 @angle:type1 $atom:id15 $atom:id12 $atom:id37 + $angle:id31 @angle:type1 $atom:id10 $atom:id13 $atom:id14 + $angle:id32 @angle:type1 $atom:id13 $atom:id14 $atom:id17 + $angle:id33 @angle:type1 $atom:id13 $atom:id14 $atom:id15 + $angle:id34 @angle:type1 $atom:id15 $atom:id14 $atom:id17 + $angle:id35 @angle:type1 $atom:id12 $atom:id15 $atom:id14 + $angle:id36 @angle:type1 $atom:id12 $atom:id15 $atom:id16 + $angle:id37 @angle:type1 $atom:id14 $atom:id15 $atom:id16 + $angle:id38 @angle:type1 $atom:id15 $atom:id16 $atom:id19 + $angle:id39 @angle:type1 $atom:id15 $atom:id16 $atom:id41 + $angle:id40 @angle:type1 $atom:id19 $atom:id16 $atom:id41 + $angle:id41 @angle:type1 $atom:id14 $atom:id17 $atom:id18 + $angle:id42 @angle:type1 $atom:id17 $atom:id18 $atom:id21 + $angle:id43 @angle:type1 $atom:id17 $atom:id18 $atom:id19 + $angle:id44 @angle:type1 $atom:id19 $atom:id18 $atom:id21 + $angle:id45 @angle:type1 $atom:id16 $atom:id19 $atom:id18 + $angle:id46 @angle:type1 $atom:id16 $atom:id19 $atom:id20 + $angle:id47 @angle:type1 $atom:id18 $atom:id19 $atom:id20 + $angle:id48 @angle:type1 $atom:id19 $atom:id20 $atom:id23 + $angle:id49 @angle:type1 $atom:id19 $atom:id20 $atom:id45 + $angle:id50 @angle:type1 $atom:id23 $atom:id20 $atom:id45 + $angle:id51 @angle:type1 $atom:id18 $atom:id21 $atom:id22 + $angle:id52 @angle:type1 $atom:id1 $atom:id22 $atom:id21 + $angle:id53 @angle:type1 $atom:id1 $atom:id22 $atom:id23 + $angle:id54 @angle:type1 $atom:id21 $atom:id22 $atom:id23 + $angle:id55 @angle:type1 $atom:id20 $atom:id23 $atom:id22 + $angle:id56 @angle:type1 $atom:id20 $atom:id23 $atom:id24 + $angle:id57 @angle:type1 $atom:id22 $atom:id23 $atom:id24 + $angle:id58 @angle:type1 $atom:id3 $atom:id24 $atom:id23 + $angle:id59 @angle:type1 $atom:id3 $atom:id24 $atom:id25 + $angle:id60 @angle:type1 $atom:id23 $atom:id24 $atom:id25 + $angle:id61 @angle:type1 $atom:id24 $atom:id25 $atom:id26 + $angle:id62 @angle:type1 $atom:id24 $atom:id25 $atom:id46 + $angle:id63 @angle:type1 $atom:id26 $atom:id25 $atom:id46 + $angle:id64 @angle:type1 $atom:id25 $atom:id26 $atom:id27 + $angle:id65 @angle:type1 $atom:id25 $atom:id26 $atom:id29 + $angle:id66 @angle:type1 $atom:id27 $atom:id26 $atom:id29 + $angle:id67 @angle:type1 $atom:id26 $atom:id27 $atom:id48 + $angle:id68 @angle:type1 $atom:id26 $atom:id27 $atom:id28 + $angle:id69 @angle:type1 $atom:id28 $atom:id27 $atom:id48 + $angle:id70 @angle:type1 $atom:id27 $atom:id28 $atom:id31 + $angle:id71 @angle:type1 $atom:id27 $atom:id28 $atom:id53 + $angle:id72 @angle:type1 $atom:id31 $atom:id28 $atom:id53 + $angle:id73 @angle:type1 $atom:id4 $atom:id29 $atom:id26 + $angle:id74 @angle:type1 $atom:id4 $atom:id29 $atom:id30 + $angle:id75 @angle:type1 $atom:id26 $atom:id29 $atom:id30 + $angle:id76 @angle:type1 $atom:id29 $atom:id30 $atom:id31 + $angle:id77 @angle:type1 $atom:id29 $atom:id30 $atom:id33 + $angle:id78 @angle:type1 $atom:id31 $atom:id30 $atom:id33 + $angle:id79 @angle:type1 $atom:id28 $atom:id31 $atom:id30 + $angle:id80 @angle:type1 $atom:id28 $atom:id31 $atom:id32 + $angle:id81 @angle:type1 $atom:id30 $atom:id31 $atom:id32 + $angle:id82 @angle:type1 $atom:id31 $atom:id32 $atom:id57 + $angle:id83 @angle:type1 $atom:id31 $atom:id32 $atom:id35 + $angle:id84 @angle:type1 $atom:id35 $atom:id32 $atom:id57 + $angle:id85 @angle:type1 $atom:id8 $atom:id33 $atom:id30 + $angle:id86 @angle:type1 $atom:id8 $atom:id33 $atom:id34 + $angle:id87 @angle:type1 $atom:id30 $atom:id33 $atom:id34 + $angle:id88 @angle:type1 $atom:id33 $atom:id34 $atom:id37 + $angle:id89 @angle:type1 $atom:id33 $atom:id34 $atom:id35 + $angle:id90 @angle:type1 $atom:id35 $atom:id34 $atom:id37 + $angle:id91 @angle:type1 $atom:id32 $atom:id35 $atom:id34 + $angle:id92 @angle:type1 $atom:id32 $atom:id35 $atom:id36 + $angle:id93 @angle:type1 $atom:id34 $atom:id35 $atom:id36 + $angle:id94 @angle:type1 $atom:id35 $atom:id36 $atom:id39 + $angle:id95 @angle:type1 $atom:id35 $atom:id36 $atom:id61 + $angle:id96 @angle:type1 $atom:id39 $atom:id36 $atom:id61 + $angle:id97 @angle:type1 $atom:id12 $atom:id37 $atom:id34 + $angle:id98 @angle:type1 $atom:id12 $atom:id37 $atom:id38 + $angle:id99 @angle:type1 $atom:id34 $atom:id37 $atom:id38 + $angle:id100 @angle:type1 $atom:id37 $atom:id38 $atom:id41 + $angle:id101 @angle:type1 $atom:id37 $atom:id38 $atom:id39 + $angle:id102 @angle:type1 $atom:id39 $atom:id38 $atom:id41 + $angle:id103 @angle:type1 $atom:id36 $atom:id39 $atom:id38 + $angle:id104 @angle:type1 $atom:id36 $atom:id39 $atom:id40 + $angle:id105 @angle:type1 $atom:id38 $atom:id39 $atom:id40 + $angle:id106 @angle:type1 $atom:id39 $atom:id40 $atom:id43 + $angle:id107 @angle:type1 $atom:id39 $atom:id40 $atom:id65 + $angle:id108 @angle:type1 $atom:id43 $atom:id40 $atom:id65 + $angle:id109 @angle:type1 $atom:id16 $atom:id41 $atom:id38 + $angle:id110 @angle:type1 $atom:id16 $atom:id41 $atom:id42 + $angle:id111 @angle:type1 $atom:id38 $atom:id41 $atom:id42 + $angle:id112 @angle:type1 $atom:id41 $atom:id42 $atom:id45 + $angle:id113 @angle:type1 $atom:id41 $atom:id42 $atom:id43 + $angle:id114 @angle:type1 $atom:id43 $atom:id42 $atom:id45 + $angle:id115 @angle:type1 $atom:id40 $atom:id43 $atom:id42 + $angle:id116 @angle:type1 $atom:id40 $atom:id43 $atom:id44 + $angle:id117 @angle:type1 $atom:id42 $atom:id43 $atom:id44 + $angle:id118 @angle:type1 $atom:id43 $atom:id44 $atom:id47 + $angle:id119 @angle:type1 $atom:id43 $atom:id44 $atom:id69 + $angle:id120 @angle:type1 $atom:id47 $atom:id44 $atom:id69 + $angle:id121 @angle:type1 $atom:id20 $atom:id45 $atom:id42 + $angle:id122 @angle:type1 $atom:id20 $atom:id45 $atom:id46 + $angle:id123 @angle:type1 $atom:id42 $atom:id45 $atom:id46 + $angle:id124 @angle:type1 $atom:id25 $atom:id46 $atom:id45 + $angle:id125 @angle:type1 $atom:id25 $atom:id46 $atom:id47 + $angle:id126 @angle:type1 $atom:id45 $atom:id46 $atom:id47 + $angle:id127 @angle:type1 $atom:id44 $atom:id47 $atom:id46 + $angle:id128 @angle:type1 $atom:id44 $atom:id47 $atom:id48 + $angle:id129 @angle:type1 $atom:id46 $atom:id47 $atom:id48 + $angle:id130 @angle:type1 $atom:id27 $atom:id48 $atom:id47 + $angle:id131 @angle:type1 $atom:id27 $atom:id48 $atom:id49 + $angle:id132 @angle:type1 $atom:id47 $atom:id48 $atom:id49 + $angle:id133 @angle:type1 $atom:id48 $atom:id49 $atom:id50 + $angle:id134 @angle:type1 $atom:id48 $atom:id49 $atom:id70 + $angle:id135 @angle:type1 $atom:id50 $atom:id49 $atom:id70 + $angle:id136 @angle:type1 $atom:id49 $atom:id50 $atom:id51 + $angle:id137 @angle:type1 $atom:id49 $atom:id50 $atom:id53 + $angle:id138 @angle:type1 $atom:id51 $atom:id50 $atom:id53 + $angle:id139 @angle:type1 $atom:id50 $atom:id51 $atom:id72 + $angle:id140 @angle:type1 $atom:id50 $atom:id51 $atom:id52 + $angle:id141 @angle:type1 $atom:id52 $atom:id51 $atom:id72 + $angle:id142 @angle:type1 $atom:id51 $atom:id52 $atom:id55 + $angle:id143 @angle:type1 $atom:id28 $atom:id53 $atom:id50 + $angle:id144 @angle:type1 $atom:id28 $atom:id53 $atom:id54 + $angle:id145 @angle:type1 $atom:id50 $atom:id53 $atom:id54 + $angle:id146 @angle:type1 $atom:id53 $atom:id54 $atom:id55 + $angle:id147 @angle:type1 $atom:id53 $atom:id54 $atom:id57 + $angle:id148 @angle:type1 $atom:id55 $atom:id54 $atom:id57 + $angle:id149 @angle:type1 $atom:id52 $atom:id55 $atom:id54 + $angle:id150 @angle:type1 $atom:id52 $atom:id55 $atom:id56 + $angle:id151 @angle:type1 $atom:id54 $atom:id55 $atom:id56 + $angle:id152 @angle:type1 $atom:id55 $atom:id56 $atom:id59 + $angle:id153 @angle:type1 $atom:id32 $atom:id57 $atom:id54 + $angle:id154 @angle:type1 $atom:id32 $atom:id57 $atom:id58 + $angle:id155 @angle:type1 $atom:id54 $atom:id57 $atom:id58 + $angle:id156 @angle:type1 $atom:id57 $atom:id58 $atom:id61 + $angle:id157 @angle:type1 $atom:id57 $atom:id58 $atom:id59 + $angle:id158 @angle:type1 $atom:id59 $atom:id58 $atom:id61 + $angle:id159 @angle:type1 $atom:id56 $atom:id59 $atom:id58 + $angle:id160 @angle:type1 $atom:id56 $atom:id59 $atom:id60 + $angle:id161 @angle:type1 $atom:id58 $atom:id59 $atom:id60 + $angle:id162 @angle:type1 $atom:id59 $atom:id60 $atom:id63 + $angle:id163 @angle:type1 $atom:id36 $atom:id61 $atom:id58 + $angle:id164 @angle:type1 $atom:id36 $atom:id61 $atom:id62 + $angle:id165 @angle:type1 $atom:id58 $atom:id61 $atom:id62 + $angle:id166 @angle:type1 $atom:id61 $atom:id62 $atom:id65 + $angle:id167 @angle:type1 $atom:id61 $atom:id62 $atom:id63 + $angle:id168 @angle:type1 $atom:id63 $atom:id62 $atom:id65 + $angle:id169 @angle:type1 $atom:id60 $atom:id63 $atom:id62 + $angle:id170 @angle:type1 $atom:id60 $atom:id63 $atom:id64 + $angle:id171 @angle:type1 $atom:id62 $atom:id63 $atom:id64 + $angle:id172 @angle:type1 $atom:id63 $atom:id64 $atom:id67 + $angle:id173 @angle:type1 $atom:id40 $atom:id65 $atom:id62 + $angle:id174 @angle:type1 $atom:id40 $atom:id65 $atom:id66 + $angle:id175 @angle:type1 $atom:id62 $atom:id65 $atom:id66 + $angle:id176 @angle:type1 $atom:id65 $atom:id66 $atom:id69 + $angle:id177 @angle:type1 $atom:id65 $atom:id66 $atom:id67 + $angle:id178 @angle:type1 $atom:id67 $atom:id66 $atom:id69 + $angle:id179 @angle:type1 $atom:id64 $atom:id67 $atom:id66 + $angle:id180 @angle:type1 $atom:id64 $atom:id67 $atom:id68 + $angle:id181 @angle:type1 $atom:id66 $atom:id67 $atom:id68 + $angle:id182 @angle:type1 $atom:id67 $atom:id68 $atom:id71 + $angle:id183 @angle:type1 $atom:id44 $atom:id69 $atom:id66 + $angle:id184 @angle:type1 $atom:id44 $atom:id69 $atom:id70 + $angle:id185 @angle:type1 $atom:id66 $atom:id69 $atom:id70 + $angle:id186 @angle:type1 $atom:id49 $atom:id70 $atom:id69 + $angle:id187 @angle:type1 $atom:id49 $atom:id70 $atom:id71 + $angle:id188 @angle:type1 $atom:id69 $atom:id70 $atom:id71 + $angle:id189 @angle:type1 $atom:id68 $atom:id71 $atom:id70 + $angle:id190 @angle:type1 $atom:id68 $atom:id71 $atom:id72 + $angle:id191 @angle:type1 $atom:id70 $atom:id71 $atom:id72 + $angle:id192 @angle:type1 $atom:id51 $atom:id72 $atom:id71 + } + + write("Data Dihedrals") { + $dihedral:id1 @dihedral:type1 $atom:id22 $atom:id1 $atom:id2 $atom:id3 + $dihedral:id2 @dihedral:type1 $atom:id22 $atom:id1 $atom:id2 $atom:id5 + $dihedral:id3 @dihedral:type1 $atom:id2 $atom:id1 $atom:id22 $atom:id21 + $dihedral:id4 @dihedral:type1 $atom:id2 $atom:id1 $atom:id22 $atom:id23 + $dihedral:id5 @dihedral:type1 $atom:id1 $atom:id2 $atom:id3 $atom:id24 + $dihedral:id6 @dihedral:type1 $atom:id1 $atom:id2 $atom:id3 $atom:id4 + $dihedral:id7 @dihedral:type1 $atom:id5 $atom:id2 $atom:id3 $atom:id24 + $dihedral:id8 @dihedral:type1 $atom:id5 $atom:id2 $atom:id3 $atom:id4 + $dihedral:id9 @dihedral:type1 $atom:id1 $atom:id2 $atom:id5 $atom:id6 + $dihedral:id10 @dihedral:type1 $atom:id3 $atom:id2 $atom:id5 $atom:id6 + $dihedral:id11 @dihedral:type1 $atom:id2 $atom:id3 $atom:id24 $atom:id23 + $dihedral:id12 @dihedral:type1 $atom:id2 $atom:id3 $atom:id24 $atom:id25 + $dihedral:id13 @dihedral:type1 $atom:id4 $atom:id3 $atom:id24 $atom:id23 + $dihedral:id14 @dihedral:type1 $atom:id4 $atom:id3 $atom:id24 $atom:id25 + $dihedral:id15 @dihedral:type1 $atom:id2 $atom:id3 $atom:id4 $atom:id7 + $dihedral:id16 @dihedral:type1 $atom:id2 $atom:id3 $atom:id4 $atom:id29 + $dihedral:id17 @dihedral:type1 $atom:id24 $atom:id3 $atom:id4 $atom:id7 + $dihedral:id18 @dihedral:type1 $atom:id24 $atom:id3 $atom:id4 $atom:id29 + $dihedral:id19 @dihedral:type1 $atom:id3 $atom:id4 $atom:id7 $atom:id6 + $dihedral:id20 @dihedral:type1 $atom:id3 $atom:id4 $atom:id7 $atom:id8 + $dihedral:id21 @dihedral:type1 $atom:id29 $atom:id4 $atom:id7 $atom:id6 + $dihedral:id22 @dihedral:type1 $atom:id29 $atom:id4 $atom:id7 $atom:id8 + $dihedral:id23 @dihedral:type1 $atom:id3 $atom:id4 $atom:id29 $atom:id26 + $dihedral:id24 @dihedral:type1 $atom:id3 $atom:id4 $atom:id29 $atom:id30 + $dihedral:id25 @dihedral:type1 $atom:id7 $atom:id4 $atom:id29 $atom:id26 + $dihedral:id26 @dihedral:type1 $atom:id7 $atom:id4 $atom:id29 $atom:id30 + $dihedral:id27 @dihedral:type1 $atom:id2 $atom:id5 $atom:id6 $atom:id7 + $dihedral:id28 @dihedral:type1 $atom:id2 $atom:id5 $atom:id6 $atom:id9 + $dihedral:id29 @dihedral:type1 $atom:id5 $atom:id6 $atom:id7 $atom:id4 + $dihedral:id30 @dihedral:type1 $atom:id5 $atom:id6 $atom:id7 $atom:id8 + $dihedral:id31 @dihedral:type1 $atom:id9 $atom:id6 $atom:id7 $atom:id4 + $dihedral:id32 @dihedral:type1 $atom:id9 $atom:id6 $atom:id7 $atom:id8 + $dihedral:id33 @dihedral:type1 $atom:id5 $atom:id6 $atom:id9 $atom:id10 + $dihedral:id34 @dihedral:type1 $atom:id7 $atom:id6 $atom:id9 $atom:id10 + $dihedral:id35 @dihedral:type1 $atom:id4 $atom:id7 $atom:id8 $atom:id33 + $dihedral:id36 @dihedral:type1 $atom:id4 $atom:id7 $atom:id8 $atom:id11 + $dihedral:id37 @dihedral:type1 $atom:id6 $atom:id7 $atom:id8 $atom:id33 + $dihedral:id38 @dihedral:type1 $atom:id6 $atom:id7 $atom:id8 $atom:id11 + $dihedral:id39 @dihedral:type1 $atom:id7 $atom:id8 $atom:id33 $atom:id30 + $dihedral:id40 @dihedral:type1 $atom:id7 $atom:id8 $atom:id33 $atom:id34 + $dihedral:id41 @dihedral:type1 $atom:id11 $atom:id8 $atom:id33 $atom:id30 + $dihedral:id42 @dihedral:type1 $atom:id11 $atom:id8 $atom:id33 $atom:id34 + $dihedral:id43 @dihedral:type1 $atom:id7 $atom:id8 $atom:id11 $atom:id10 + $dihedral:id44 @dihedral:type1 $atom:id7 $atom:id8 $atom:id11 $atom:id12 + $dihedral:id45 @dihedral:type1 $atom:id33 $atom:id8 $atom:id11 $atom:id10 + $dihedral:id46 @dihedral:type1 $atom:id33 $atom:id8 $atom:id11 $atom:id12 + $dihedral:id47 @dihedral:type1 $atom:id6 $atom:id9 $atom:id10 $atom:id13 + $dihedral:id48 @dihedral:type1 $atom:id6 $atom:id9 $atom:id10 $atom:id11 + $dihedral:id49 @dihedral:type1 $atom:id9 $atom:id10 $atom:id13 $atom:id14 + $dihedral:id50 @dihedral:type1 $atom:id11 $atom:id10 $atom:id13 $atom:id14 + $dihedral:id51 @dihedral:type1 $atom:id9 $atom:id10 $atom:id11 $atom:id8 + $dihedral:id52 @dihedral:type1 $atom:id9 $atom:id10 $atom:id11 $atom:id12 + $dihedral:id53 @dihedral:type1 $atom:id13 $atom:id10 $atom:id11 $atom:id8 + $dihedral:id54 @dihedral:type1 $atom:id13 $atom:id10 $atom:id11 $atom:id12 + $dihedral:id55 @dihedral:type1 $atom:id8 $atom:id11 $atom:id12 $atom:id15 + $dihedral:id56 @dihedral:type1 $atom:id8 $atom:id11 $atom:id12 $atom:id37 + $dihedral:id57 @dihedral:type1 $atom:id10 $atom:id11 $atom:id12 $atom:id15 + $dihedral:id58 @dihedral:type1 $atom:id10 $atom:id11 $atom:id12 $atom:id37 + $dihedral:id59 @dihedral:type1 $atom:id11 $atom:id12 $atom:id15 $atom:id14 + $dihedral:id60 @dihedral:type1 $atom:id11 $atom:id12 $atom:id15 $atom:id16 + $dihedral:id61 @dihedral:type1 $atom:id37 $atom:id12 $atom:id15 $atom:id14 + $dihedral:id62 @dihedral:type1 $atom:id37 $atom:id12 $atom:id15 $atom:id16 + $dihedral:id63 @dihedral:type1 $atom:id11 $atom:id12 $atom:id37 $atom:id34 + $dihedral:id64 @dihedral:type1 $atom:id11 $atom:id12 $atom:id37 $atom:id38 + $dihedral:id65 @dihedral:type1 $atom:id15 $atom:id12 $atom:id37 $atom:id34 + $dihedral:id66 @dihedral:type1 $atom:id15 $atom:id12 $atom:id37 $atom:id38 + $dihedral:id67 @dihedral:type1 $atom:id10 $atom:id13 $atom:id14 $atom:id17 + $dihedral:id68 @dihedral:type1 $atom:id10 $atom:id13 $atom:id14 $atom:id15 + $dihedral:id69 @dihedral:type1 $atom:id13 $atom:id14 $atom:id17 $atom:id18 + $dihedral:id70 @dihedral:type1 $atom:id15 $atom:id14 $atom:id17 $atom:id18 + $dihedral:id71 @dihedral:type1 $atom:id13 $atom:id14 $atom:id15 $atom:id12 + $dihedral:id72 @dihedral:type1 $atom:id13 $atom:id14 $atom:id15 $atom:id16 + $dihedral:id73 @dihedral:type1 $atom:id17 $atom:id14 $atom:id15 $atom:id12 + $dihedral:id74 @dihedral:type1 $atom:id17 $atom:id14 $atom:id15 $atom:id16 + $dihedral:id75 @dihedral:type1 $atom:id12 $atom:id15 $atom:id16 $atom:id19 + $dihedral:id76 @dihedral:type1 $atom:id12 $atom:id15 $atom:id16 $atom:id41 + $dihedral:id77 @dihedral:type1 $atom:id14 $atom:id15 $atom:id16 $atom:id19 + $dihedral:id78 @dihedral:type1 $atom:id14 $atom:id15 $atom:id16 $atom:id41 + $dihedral:id79 @dihedral:type1 $atom:id15 $atom:id16 $atom:id19 $atom:id18 + $dihedral:id80 @dihedral:type1 $atom:id15 $atom:id16 $atom:id19 $atom:id20 + $dihedral:id81 @dihedral:type1 $atom:id41 $atom:id16 $atom:id19 $atom:id18 + $dihedral:id82 @dihedral:type1 $atom:id41 $atom:id16 $atom:id19 $atom:id20 + $dihedral:id83 @dihedral:type1 $atom:id15 $atom:id16 $atom:id41 $atom:id38 + $dihedral:id84 @dihedral:type1 $atom:id15 $atom:id16 $atom:id41 $atom:id42 + $dihedral:id85 @dihedral:type1 $atom:id19 $atom:id16 $atom:id41 $atom:id38 + $dihedral:id86 @dihedral:type1 $atom:id19 $atom:id16 $atom:id41 $atom:id42 + $dihedral:id87 @dihedral:type1 $atom:id14 $atom:id17 $atom:id18 $atom:id21 + $dihedral:id88 @dihedral:type1 $atom:id14 $atom:id17 $atom:id18 $atom:id19 + $dihedral:id89 @dihedral:type1 $atom:id17 $atom:id18 $atom:id21 $atom:id22 + $dihedral:id90 @dihedral:type1 $atom:id19 $atom:id18 $atom:id21 $atom:id22 + $dihedral:id91 @dihedral:type1 $atom:id17 $atom:id18 $atom:id19 $atom:id16 + $dihedral:id92 @dihedral:type1 $atom:id17 $atom:id18 $atom:id19 $atom:id20 + $dihedral:id93 @dihedral:type1 $atom:id21 $atom:id18 $atom:id19 $atom:id16 + $dihedral:id94 @dihedral:type1 $atom:id21 $atom:id18 $atom:id19 $atom:id20 + $dihedral:id95 @dihedral:type1 $atom:id16 $atom:id19 $atom:id20 $atom:id23 + $dihedral:id96 @dihedral:type1 $atom:id16 $atom:id19 $atom:id20 $atom:id45 + $dihedral:id97 @dihedral:type1 $atom:id18 $atom:id19 $atom:id20 $atom:id23 + $dihedral:id98 @dihedral:type1 $atom:id18 $atom:id19 $atom:id20 $atom:id45 + $dihedral:id99 @dihedral:type1 $atom:id19 $atom:id20 $atom:id23 $atom:id22 + $dihedral:id100 @dihedral:type1 $atom:id19 $atom:id20 $atom:id23 $atom:id24 + $dihedral:id101 @dihedral:type1 $atom:id45 $atom:id20 $atom:id23 $atom:id22 + $dihedral:id102 @dihedral:type1 $atom:id45 $atom:id20 $atom:id23 $atom:id24 + $dihedral:id103 @dihedral:type1 $atom:id19 $atom:id20 $atom:id45 $atom:id42 + $dihedral:id104 @dihedral:type1 $atom:id19 $atom:id20 $atom:id45 $atom:id46 + $dihedral:id105 @dihedral:type1 $atom:id23 $atom:id20 $atom:id45 $atom:id42 + $dihedral:id106 @dihedral:type1 $atom:id23 $atom:id20 $atom:id45 $atom:id46 + $dihedral:id107 @dihedral:type1 $atom:id18 $atom:id21 $atom:id22 $atom:id1 + $dihedral:id108 @dihedral:type1 $atom:id18 $atom:id21 $atom:id22 $atom:id23 + $dihedral:id109 @dihedral:type1 $atom:id1 $atom:id22 $atom:id23 $atom:id20 + $dihedral:id110 @dihedral:type1 $atom:id1 $atom:id22 $atom:id23 $atom:id24 + $dihedral:id111 @dihedral:type1 $atom:id21 $atom:id22 $atom:id23 $atom:id20 + $dihedral:id112 @dihedral:type1 $atom:id21 $atom:id22 $atom:id23 $atom:id24 + $dihedral:id113 @dihedral:type1 $atom:id20 $atom:id23 $atom:id24 $atom:id3 + $dihedral:id114 @dihedral:type1 $atom:id20 $atom:id23 $atom:id24 $atom:id25 + $dihedral:id115 @dihedral:type1 $atom:id22 $atom:id23 $atom:id24 $atom:id3 + $dihedral:id116 @dihedral:type1 $atom:id22 $atom:id23 $atom:id24 $atom:id25 + $dihedral:id117 @dihedral:type1 $atom:id3 $atom:id24 $atom:id25 $atom:id26 + $dihedral:id118 @dihedral:type1 $atom:id3 $atom:id24 $atom:id25 $atom:id46 + $dihedral:id119 @dihedral:type1 $atom:id23 $atom:id24 $atom:id25 $atom:id26 + $dihedral:id120 @dihedral:type1 $atom:id23 $atom:id24 $atom:id25 $atom:id46 + $dihedral:id121 @dihedral:type1 $atom:id24 $atom:id25 $atom:id26 $atom:id27 + $dihedral:id122 @dihedral:type1 $atom:id24 $atom:id25 $atom:id26 $atom:id29 + $dihedral:id123 @dihedral:type1 $atom:id46 $atom:id25 $atom:id26 $atom:id27 + $dihedral:id124 @dihedral:type1 $atom:id46 $atom:id25 $atom:id26 $atom:id29 + $dihedral:id125 @dihedral:type1 $atom:id24 $atom:id25 $atom:id46 $atom:id45 + $dihedral:id126 @dihedral:type1 $atom:id24 $atom:id25 $atom:id46 $atom:id47 + $dihedral:id127 @dihedral:type1 $atom:id26 $atom:id25 $atom:id46 $atom:id45 + $dihedral:id128 @dihedral:type1 $atom:id26 $atom:id25 $atom:id46 $atom:id47 + $dihedral:id129 @dihedral:type1 $atom:id25 $atom:id26 $atom:id27 $atom:id48 + $dihedral:id130 @dihedral:type1 $atom:id25 $atom:id26 $atom:id27 $atom:id28 + $dihedral:id131 @dihedral:type1 $atom:id29 $atom:id26 $atom:id27 $atom:id48 + $dihedral:id132 @dihedral:type1 $atom:id29 $atom:id26 $atom:id27 $atom:id28 + $dihedral:id133 @dihedral:type1 $atom:id25 $atom:id26 $atom:id29 $atom:id4 + $dihedral:id134 @dihedral:type1 $atom:id25 $atom:id26 $atom:id29 $atom:id30 + $dihedral:id135 @dihedral:type1 $atom:id27 $atom:id26 $atom:id29 $atom:id4 + $dihedral:id136 @dihedral:type1 $atom:id27 $atom:id26 $atom:id29 $atom:id30 + $dihedral:id137 @dihedral:type1 $atom:id26 $atom:id27 $atom:id48 $atom:id47 + $dihedral:id138 @dihedral:type1 $atom:id26 $atom:id27 $atom:id48 $atom:id49 + $dihedral:id139 @dihedral:type1 $atom:id28 $atom:id27 $atom:id48 $atom:id47 + $dihedral:id140 @dihedral:type1 $atom:id28 $atom:id27 $atom:id48 $atom:id49 + $dihedral:id141 @dihedral:type1 $atom:id26 $atom:id27 $atom:id28 $atom:id31 + $dihedral:id142 @dihedral:type1 $atom:id26 $atom:id27 $atom:id28 $atom:id53 + $dihedral:id143 @dihedral:type1 $atom:id48 $atom:id27 $atom:id28 $atom:id31 + $dihedral:id144 @dihedral:type1 $atom:id48 $atom:id27 $atom:id28 $atom:id53 + $dihedral:id145 @dihedral:type1 $atom:id27 $atom:id28 $atom:id31 $atom:id30 + $dihedral:id146 @dihedral:type1 $atom:id27 $atom:id28 $atom:id31 $atom:id32 + $dihedral:id147 @dihedral:type1 $atom:id53 $atom:id28 $atom:id31 $atom:id30 + $dihedral:id148 @dihedral:type1 $atom:id53 $atom:id28 $atom:id31 $atom:id32 + $dihedral:id149 @dihedral:type1 $atom:id27 $atom:id28 $atom:id53 $atom:id50 + $dihedral:id150 @dihedral:type1 $atom:id27 $atom:id28 $atom:id53 $atom:id54 + $dihedral:id151 @dihedral:type1 $atom:id31 $atom:id28 $atom:id53 $atom:id50 + $dihedral:id152 @dihedral:type1 $atom:id31 $atom:id28 $atom:id53 $atom:id54 + $dihedral:id153 @dihedral:type1 $atom:id4 $atom:id29 $atom:id30 $atom:id31 + $dihedral:id154 @dihedral:type1 $atom:id4 $atom:id29 $atom:id30 $atom:id33 + $dihedral:id155 @dihedral:type1 $atom:id26 $atom:id29 $atom:id30 $atom:id31 + $dihedral:id156 @dihedral:type1 $atom:id26 $atom:id29 $atom:id30 $atom:id33 + $dihedral:id157 @dihedral:type1 $atom:id29 $atom:id30 $atom:id31 $atom:id28 + $dihedral:id158 @dihedral:type1 $atom:id29 $atom:id30 $atom:id31 $atom:id32 + $dihedral:id159 @dihedral:type1 $atom:id33 $atom:id30 $atom:id31 $atom:id28 + $dihedral:id160 @dihedral:type1 $atom:id33 $atom:id30 $atom:id31 $atom:id32 + $dihedral:id161 @dihedral:type1 $atom:id29 $atom:id30 $atom:id33 $atom:id8 + $dihedral:id162 @dihedral:type1 $atom:id29 $atom:id30 $atom:id33 $atom:id34 + $dihedral:id163 @dihedral:type1 $atom:id31 $atom:id30 $atom:id33 $atom:id8 + $dihedral:id164 @dihedral:type1 $atom:id31 $atom:id30 $atom:id33 $atom:id34 + $dihedral:id165 @dihedral:type1 $atom:id28 $atom:id31 $atom:id32 $atom:id57 + $dihedral:id166 @dihedral:type1 $atom:id28 $atom:id31 $atom:id32 $atom:id35 + $dihedral:id167 @dihedral:type1 $atom:id30 $atom:id31 $atom:id32 $atom:id57 + $dihedral:id168 @dihedral:type1 $atom:id30 $atom:id31 $atom:id32 $atom:id35 + $dihedral:id169 @dihedral:type1 $atom:id31 $atom:id32 $atom:id57 $atom:id54 + $dihedral:id170 @dihedral:type1 $atom:id31 $atom:id32 $atom:id57 $atom:id58 + $dihedral:id171 @dihedral:type1 $atom:id35 $atom:id32 $atom:id57 $atom:id54 + $dihedral:id172 @dihedral:type1 $atom:id35 $atom:id32 $atom:id57 $atom:id58 + $dihedral:id173 @dihedral:type1 $atom:id31 $atom:id32 $atom:id35 $atom:id34 + $dihedral:id174 @dihedral:type1 $atom:id31 $atom:id32 $atom:id35 $atom:id36 + $dihedral:id175 @dihedral:type1 $atom:id57 $atom:id32 $atom:id35 $atom:id34 + $dihedral:id176 @dihedral:type1 $atom:id57 $atom:id32 $atom:id35 $atom:id36 + $dihedral:id177 @dihedral:type1 $atom:id8 $atom:id33 $atom:id34 $atom:id37 + $dihedral:id178 @dihedral:type1 $atom:id8 $atom:id33 $atom:id34 $atom:id35 + $dihedral:id179 @dihedral:type1 $atom:id30 $atom:id33 $atom:id34 $atom:id37 + $dihedral:id180 @dihedral:type1 $atom:id30 $atom:id33 $atom:id34 $atom:id35 + $dihedral:id181 @dihedral:type1 $atom:id33 $atom:id34 $atom:id37 $atom:id12 + $dihedral:id182 @dihedral:type1 $atom:id33 $atom:id34 $atom:id37 $atom:id38 + $dihedral:id183 @dihedral:type1 $atom:id35 $atom:id34 $atom:id37 $atom:id12 + $dihedral:id184 @dihedral:type1 $atom:id35 $atom:id34 $atom:id37 $atom:id38 + $dihedral:id185 @dihedral:type1 $atom:id33 $atom:id34 $atom:id35 $atom:id32 + $dihedral:id186 @dihedral:type1 $atom:id33 $atom:id34 $atom:id35 $atom:id36 + $dihedral:id187 @dihedral:type1 $atom:id37 $atom:id34 $atom:id35 $atom:id32 + $dihedral:id188 @dihedral:type1 $atom:id37 $atom:id34 $atom:id35 $atom:id36 + $dihedral:id189 @dihedral:type1 $atom:id32 $atom:id35 $atom:id36 $atom:id39 + $dihedral:id190 @dihedral:type1 $atom:id32 $atom:id35 $atom:id36 $atom:id61 + $dihedral:id191 @dihedral:type1 $atom:id34 $atom:id35 $atom:id36 $atom:id39 + $dihedral:id192 @dihedral:type1 $atom:id34 $atom:id35 $atom:id36 $atom:id61 + $dihedral:id193 @dihedral:type1 $atom:id35 $atom:id36 $atom:id39 $atom:id38 + $dihedral:id194 @dihedral:type1 $atom:id35 $atom:id36 $atom:id39 $atom:id40 + $dihedral:id195 @dihedral:type1 $atom:id61 $atom:id36 $atom:id39 $atom:id38 + $dihedral:id196 @dihedral:type1 $atom:id61 $atom:id36 $atom:id39 $atom:id40 + $dihedral:id197 @dihedral:type1 $atom:id35 $atom:id36 $atom:id61 $atom:id58 + $dihedral:id198 @dihedral:type1 $atom:id35 $atom:id36 $atom:id61 $atom:id62 + $dihedral:id199 @dihedral:type1 $atom:id39 $atom:id36 $atom:id61 $atom:id58 + $dihedral:id200 @dihedral:type1 $atom:id39 $atom:id36 $atom:id61 $atom:id62 + $dihedral:id201 @dihedral:type1 $atom:id12 $atom:id37 $atom:id38 $atom:id41 + $dihedral:id202 @dihedral:type1 $atom:id12 $atom:id37 $atom:id38 $atom:id39 + $dihedral:id203 @dihedral:type1 $atom:id34 $atom:id37 $atom:id38 $atom:id41 + $dihedral:id204 @dihedral:type1 $atom:id34 $atom:id37 $atom:id38 $atom:id39 + $dihedral:id205 @dihedral:type1 $atom:id37 $atom:id38 $atom:id41 $atom:id16 + $dihedral:id206 @dihedral:type1 $atom:id37 $atom:id38 $atom:id41 $atom:id42 + $dihedral:id207 @dihedral:type1 $atom:id39 $atom:id38 $atom:id41 $atom:id16 + $dihedral:id208 @dihedral:type1 $atom:id39 $atom:id38 $atom:id41 $atom:id42 + $dihedral:id209 @dihedral:type1 $atom:id37 $atom:id38 $atom:id39 $atom:id36 + $dihedral:id210 @dihedral:type1 $atom:id37 $atom:id38 $atom:id39 $atom:id40 + $dihedral:id211 @dihedral:type1 $atom:id41 $atom:id38 $atom:id39 $atom:id36 + $dihedral:id212 @dihedral:type1 $atom:id41 $atom:id38 $atom:id39 $atom:id40 + $dihedral:id213 @dihedral:type1 $atom:id36 $atom:id39 $atom:id40 $atom:id43 + $dihedral:id214 @dihedral:type1 $atom:id36 $atom:id39 $atom:id40 $atom:id65 + $dihedral:id215 @dihedral:type1 $atom:id38 $atom:id39 $atom:id40 $atom:id43 + $dihedral:id216 @dihedral:type1 $atom:id38 $atom:id39 $atom:id40 $atom:id65 + $dihedral:id217 @dihedral:type1 $atom:id39 $atom:id40 $atom:id43 $atom:id42 + $dihedral:id218 @dihedral:type1 $atom:id39 $atom:id40 $atom:id43 $atom:id44 + $dihedral:id219 @dihedral:type1 $atom:id65 $atom:id40 $atom:id43 $atom:id42 + $dihedral:id220 @dihedral:type1 $atom:id65 $atom:id40 $atom:id43 $atom:id44 + $dihedral:id221 @dihedral:type1 $atom:id39 $atom:id40 $atom:id65 $atom:id62 + $dihedral:id222 @dihedral:type1 $atom:id39 $atom:id40 $atom:id65 $atom:id66 + $dihedral:id223 @dihedral:type1 $atom:id43 $atom:id40 $atom:id65 $atom:id62 + $dihedral:id224 @dihedral:type1 $atom:id43 $atom:id40 $atom:id65 $atom:id66 + $dihedral:id225 @dihedral:type1 $atom:id16 $atom:id41 $atom:id42 $atom:id45 + $dihedral:id226 @dihedral:type1 $atom:id16 $atom:id41 $atom:id42 $atom:id43 + $dihedral:id227 @dihedral:type1 $atom:id38 $atom:id41 $atom:id42 $atom:id45 + $dihedral:id228 @dihedral:type1 $atom:id38 $atom:id41 $atom:id42 $atom:id43 + $dihedral:id229 @dihedral:type1 $atom:id41 $atom:id42 $atom:id45 $atom:id20 + $dihedral:id230 @dihedral:type1 $atom:id41 $atom:id42 $atom:id45 $atom:id46 + $dihedral:id231 @dihedral:type1 $atom:id43 $atom:id42 $atom:id45 $atom:id20 + $dihedral:id232 @dihedral:type1 $atom:id43 $atom:id42 $atom:id45 $atom:id46 + $dihedral:id233 @dihedral:type1 $atom:id41 $atom:id42 $atom:id43 $atom:id40 + $dihedral:id234 @dihedral:type1 $atom:id41 $atom:id42 $atom:id43 $atom:id44 + $dihedral:id235 @dihedral:type1 $atom:id45 $atom:id42 $atom:id43 $atom:id40 + $dihedral:id236 @dihedral:type1 $atom:id45 $atom:id42 $atom:id43 $atom:id44 + $dihedral:id237 @dihedral:type1 $atom:id40 $atom:id43 $atom:id44 $atom:id47 + $dihedral:id238 @dihedral:type1 $atom:id40 $atom:id43 $atom:id44 $atom:id69 + $dihedral:id239 @dihedral:type1 $atom:id42 $atom:id43 $atom:id44 $atom:id47 + $dihedral:id240 @dihedral:type1 $atom:id42 $atom:id43 $atom:id44 $atom:id69 + $dihedral:id241 @dihedral:type1 $atom:id43 $atom:id44 $atom:id47 $atom:id46 + $dihedral:id242 @dihedral:type1 $atom:id43 $atom:id44 $atom:id47 $atom:id48 + $dihedral:id243 @dihedral:type1 $atom:id69 $atom:id44 $atom:id47 $atom:id46 + $dihedral:id244 @dihedral:type1 $atom:id69 $atom:id44 $atom:id47 $atom:id48 + $dihedral:id245 @dihedral:type1 $atom:id43 $atom:id44 $atom:id69 $atom:id66 + $dihedral:id246 @dihedral:type1 $atom:id43 $atom:id44 $atom:id69 $atom:id70 + $dihedral:id247 @dihedral:type1 $atom:id47 $atom:id44 $atom:id69 $atom:id66 + $dihedral:id248 @dihedral:type1 $atom:id47 $atom:id44 $atom:id69 $atom:id70 + $dihedral:id249 @dihedral:type1 $atom:id20 $atom:id45 $atom:id46 $atom:id25 + $dihedral:id250 @dihedral:type1 $atom:id20 $atom:id45 $atom:id46 $atom:id47 + $dihedral:id251 @dihedral:type1 $atom:id42 $atom:id45 $atom:id46 $atom:id25 + $dihedral:id252 @dihedral:type1 $atom:id42 $atom:id45 $atom:id46 $atom:id47 + $dihedral:id253 @dihedral:type1 $atom:id25 $atom:id46 $atom:id47 $atom:id44 + $dihedral:id254 @dihedral:type1 $atom:id25 $atom:id46 $atom:id47 $atom:id48 + $dihedral:id255 @dihedral:type1 $atom:id45 $atom:id46 $atom:id47 $atom:id44 + $dihedral:id256 @dihedral:type1 $atom:id45 $atom:id46 $atom:id47 $atom:id48 + $dihedral:id257 @dihedral:type1 $atom:id44 $atom:id47 $atom:id48 $atom:id27 + $dihedral:id258 @dihedral:type1 $atom:id44 $atom:id47 $atom:id48 $atom:id49 + $dihedral:id259 @dihedral:type1 $atom:id46 $atom:id47 $atom:id48 $atom:id27 + $dihedral:id260 @dihedral:type1 $atom:id46 $atom:id47 $atom:id48 $atom:id49 + $dihedral:id261 @dihedral:type1 $atom:id27 $atom:id48 $atom:id49 $atom:id50 + $dihedral:id262 @dihedral:type1 $atom:id27 $atom:id48 $atom:id49 $atom:id70 + $dihedral:id263 @dihedral:type1 $atom:id47 $atom:id48 $atom:id49 $atom:id50 + $dihedral:id264 @dihedral:type1 $atom:id47 $atom:id48 $atom:id49 $atom:id70 + $dihedral:id265 @dihedral:type1 $atom:id48 $atom:id49 $atom:id50 $atom:id51 + $dihedral:id266 @dihedral:type1 $atom:id48 $atom:id49 $atom:id50 $atom:id53 + $dihedral:id267 @dihedral:type1 $atom:id70 $atom:id49 $atom:id50 $atom:id51 + $dihedral:id268 @dihedral:type1 $atom:id70 $atom:id49 $atom:id50 $atom:id53 + $dihedral:id269 @dihedral:type1 $atom:id48 $atom:id49 $atom:id70 $atom:id69 + $dihedral:id270 @dihedral:type1 $atom:id48 $atom:id49 $atom:id70 $atom:id71 + $dihedral:id271 @dihedral:type1 $atom:id50 $atom:id49 $atom:id70 $atom:id69 + $dihedral:id272 @dihedral:type1 $atom:id50 $atom:id49 $atom:id70 $atom:id71 + $dihedral:id273 @dihedral:type1 $atom:id49 $atom:id50 $atom:id51 $atom:id72 + $dihedral:id274 @dihedral:type1 $atom:id49 $atom:id50 $atom:id51 $atom:id52 + $dihedral:id275 @dihedral:type1 $atom:id53 $atom:id50 $atom:id51 $atom:id72 + $dihedral:id276 @dihedral:type1 $atom:id53 $atom:id50 $atom:id51 $atom:id52 + $dihedral:id277 @dihedral:type1 $atom:id49 $atom:id50 $atom:id53 $atom:id28 + $dihedral:id278 @dihedral:type1 $atom:id49 $atom:id50 $atom:id53 $atom:id54 + $dihedral:id279 @dihedral:type1 $atom:id51 $atom:id50 $atom:id53 $atom:id28 + $dihedral:id280 @dihedral:type1 $atom:id51 $atom:id50 $atom:id53 $atom:id54 + $dihedral:id281 @dihedral:type1 $atom:id50 $atom:id51 $atom:id72 $atom:id71 + $dihedral:id282 @dihedral:type1 $atom:id52 $atom:id51 $atom:id72 $atom:id71 + $dihedral:id283 @dihedral:type1 $atom:id50 $atom:id51 $atom:id52 $atom:id55 + $dihedral:id284 @dihedral:type1 $atom:id72 $atom:id51 $atom:id52 $atom:id55 + $dihedral:id285 @dihedral:type1 $atom:id51 $atom:id52 $atom:id55 $atom:id54 + $dihedral:id286 @dihedral:type1 $atom:id51 $atom:id52 $atom:id55 $atom:id56 + $dihedral:id287 @dihedral:type1 $atom:id28 $atom:id53 $atom:id54 $atom:id55 + $dihedral:id288 @dihedral:type1 $atom:id28 $atom:id53 $atom:id54 $atom:id57 + $dihedral:id289 @dihedral:type1 $atom:id50 $atom:id53 $atom:id54 $atom:id55 + $dihedral:id290 @dihedral:type1 $atom:id50 $atom:id53 $atom:id54 $atom:id57 + $dihedral:id291 @dihedral:type1 $atom:id53 $atom:id54 $atom:id55 $atom:id52 + $dihedral:id292 @dihedral:type1 $atom:id53 $atom:id54 $atom:id55 $atom:id56 + $dihedral:id293 @dihedral:type1 $atom:id57 $atom:id54 $atom:id55 $atom:id52 + $dihedral:id294 @dihedral:type1 $atom:id57 $atom:id54 $atom:id55 $atom:id56 + $dihedral:id295 @dihedral:type1 $atom:id53 $atom:id54 $atom:id57 $atom:id32 + $dihedral:id296 @dihedral:type1 $atom:id53 $atom:id54 $atom:id57 $atom:id58 + $dihedral:id297 @dihedral:type1 $atom:id55 $atom:id54 $atom:id57 $atom:id32 + $dihedral:id298 @dihedral:type1 $atom:id55 $atom:id54 $atom:id57 $atom:id58 + $dihedral:id299 @dihedral:type1 $atom:id52 $atom:id55 $atom:id56 $atom:id59 + $dihedral:id300 @dihedral:type1 $atom:id54 $atom:id55 $atom:id56 $atom:id59 + $dihedral:id301 @dihedral:type1 $atom:id55 $atom:id56 $atom:id59 $atom:id58 + $dihedral:id302 @dihedral:type1 $atom:id55 $atom:id56 $atom:id59 $atom:id60 + $dihedral:id303 @dihedral:type1 $atom:id32 $atom:id57 $atom:id58 $atom:id61 + $dihedral:id304 @dihedral:type1 $atom:id32 $atom:id57 $atom:id58 $atom:id59 + $dihedral:id305 @dihedral:type1 $atom:id54 $atom:id57 $atom:id58 $atom:id61 + $dihedral:id306 @dihedral:type1 $atom:id54 $atom:id57 $atom:id58 $atom:id59 + $dihedral:id307 @dihedral:type1 $atom:id57 $atom:id58 $atom:id61 $atom:id36 + $dihedral:id308 @dihedral:type1 $atom:id57 $atom:id58 $atom:id61 $atom:id62 + $dihedral:id309 @dihedral:type1 $atom:id59 $atom:id58 $atom:id61 $atom:id36 + $dihedral:id310 @dihedral:type1 $atom:id59 $atom:id58 $atom:id61 $atom:id62 + $dihedral:id311 @dihedral:type1 $atom:id57 $atom:id58 $atom:id59 $atom:id56 + $dihedral:id312 @dihedral:type1 $atom:id57 $atom:id58 $atom:id59 $atom:id60 + $dihedral:id313 @dihedral:type1 $atom:id61 $atom:id58 $atom:id59 $atom:id56 + $dihedral:id314 @dihedral:type1 $atom:id61 $atom:id58 $atom:id59 $atom:id60 + $dihedral:id315 @dihedral:type1 $atom:id56 $atom:id59 $atom:id60 $atom:id63 + $dihedral:id316 @dihedral:type1 $atom:id58 $atom:id59 $atom:id60 $atom:id63 + $dihedral:id317 @dihedral:type1 $atom:id59 $atom:id60 $atom:id63 $atom:id62 + $dihedral:id318 @dihedral:type1 $atom:id59 $atom:id60 $atom:id63 $atom:id64 + $dihedral:id319 @dihedral:type1 $atom:id36 $atom:id61 $atom:id62 $atom:id65 + $dihedral:id320 @dihedral:type1 $atom:id36 $atom:id61 $atom:id62 $atom:id63 + $dihedral:id321 @dihedral:type1 $atom:id58 $atom:id61 $atom:id62 $atom:id65 + $dihedral:id322 @dihedral:type1 $atom:id58 $atom:id61 $atom:id62 $atom:id63 + $dihedral:id323 @dihedral:type1 $atom:id61 $atom:id62 $atom:id65 $atom:id40 + $dihedral:id324 @dihedral:type1 $atom:id61 $atom:id62 $atom:id65 $atom:id66 + $dihedral:id325 @dihedral:type1 $atom:id63 $atom:id62 $atom:id65 $atom:id40 + $dihedral:id326 @dihedral:type1 $atom:id63 $atom:id62 $atom:id65 $atom:id66 + $dihedral:id327 @dihedral:type1 $atom:id61 $atom:id62 $atom:id63 $atom:id60 + $dihedral:id328 @dihedral:type1 $atom:id61 $atom:id62 $atom:id63 $atom:id64 + $dihedral:id329 @dihedral:type1 $atom:id65 $atom:id62 $atom:id63 $atom:id60 + $dihedral:id330 @dihedral:type1 $atom:id65 $atom:id62 $atom:id63 $atom:id64 + $dihedral:id331 @dihedral:type1 $atom:id60 $atom:id63 $atom:id64 $atom:id67 + $dihedral:id332 @dihedral:type1 $atom:id62 $atom:id63 $atom:id64 $atom:id67 + $dihedral:id333 @dihedral:type1 $atom:id63 $atom:id64 $atom:id67 $atom:id66 + $dihedral:id334 @dihedral:type1 $atom:id63 $atom:id64 $atom:id67 $atom:id68 + $dihedral:id335 @dihedral:type1 $atom:id40 $atom:id65 $atom:id66 $atom:id69 + $dihedral:id336 @dihedral:type1 $atom:id40 $atom:id65 $atom:id66 $atom:id67 + $dihedral:id337 @dihedral:type1 $atom:id62 $atom:id65 $atom:id66 $atom:id69 + $dihedral:id338 @dihedral:type1 $atom:id62 $atom:id65 $atom:id66 $atom:id67 + $dihedral:id339 @dihedral:type1 $atom:id65 $atom:id66 $atom:id69 $atom:id44 + $dihedral:id340 @dihedral:type1 $atom:id65 $atom:id66 $atom:id69 $atom:id70 + $dihedral:id341 @dihedral:type1 $atom:id67 $atom:id66 $atom:id69 $atom:id44 + $dihedral:id342 @dihedral:type1 $atom:id67 $atom:id66 $atom:id69 $atom:id70 + $dihedral:id343 @dihedral:type1 $atom:id65 $atom:id66 $atom:id67 $atom:id64 + $dihedral:id344 @dihedral:type1 $atom:id65 $atom:id66 $atom:id67 $atom:id68 + $dihedral:id345 @dihedral:type1 $atom:id69 $atom:id66 $atom:id67 $atom:id64 + $dihedral:id346 @dihedral:type1 $atom:id69 $atom:id66 $atom:id67 $atom:id68 + $dihedral:id347 @dihedral:type1 $atom:id64 $atom:id67 $atom:id68 $atom:id71 + $dihedral:id348 @dihedral:type1 $atom:id66 $atom:id67 $atom:id68 $atom:id71 + $dihedral:id349 @dihedral:type1 $atom:id67 $atom:id68 $atom:id71 $atom:id70 + $dihedral:id350 @dihedral:type1 $atom:id67 $atom:id68 $atom:id71 $atom:id72 + $dihedral:id351 @dihedral:type1 $atom:id44 $atom:id69 $atom:id70 $atom:id49 + $dihedral:id352 @dihedral:type1 $atom:id44 $atom:id69 $atom:id70 $atom:id71 + $dihedral:id353 @dihedral:type1 $atom:id66 $atom:id69 $atom:id70 $atom:id49 + $dihedral:id354 @dihedral:type1 $atom:id66 $atom:id69 $atom:id70 $atom:id71 + $dihedral:id355 @dihedral:type1 $atom:id49 $atom:id70 $atom:id71 $atom:id68 + $dihedral:id356 @dihedral:type1 $atom:id49 $atom:id70 $atom:id71 $atom:id72 + $dihedral:id357 @dihedral:type1 $atom:id69 $atom:id70 $atom:id71 $atom:id68 + $dihedral:id358 @dihedral:type1 $atom:id69 $atom:id70 $atom:id71 $atom:id72 + $dihedral:id359 @dihedral:type1 $atom:id68 $atom:id71 $atom:id72 $atom:id51 + $dihedral:id360 @dihedral:type1 $atom:id70 $atom:id71 $atom:id72 $atom:id51 + } + +} # end of "CNT" type definition diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg new file mode 100644 index 000000000..3b79b405e Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_orig.jpg b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_orig.jpg new file mode 100644 index 000000000..1f46c1b7b Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_orig.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad.jpg b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad.jpg new file mode 100644 index 000000000..628371b0d Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnt.jpg b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnt.jpg new file mode 100644 index 000000000..3489773ad Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnt.jpg differ diff --git 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0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt new file mode 100644 index 000000000..5c1d2d417 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt @@ -0,0 +1,46 @@ +########################################################### +# Interaction of a carbon nanotube with a pair of mystery +# molecules (extracted from the cnat-cnt.data/in files). +########################################################### +# +# define the system being simulated: + +# -- init section -- +include system.in.init + +# -- atom definition section -- + +read_data system.data + +# -- settings section -- + +include system.in.settings + +# -- run section -- + + +timestep 0.05 +dump 1 all custom 2000 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# The Nose-Hoover thermostat used with "fix nvt" can produce very odd-looking +# dynamics in dilute systems with few atoms (such as this one). +# Commenting this next line out: + +# fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 + +# Alternately, I receive fewer questions if I use langevin/nve instead: +fix fxlan all langevin 300.0 300.0 1000.0 48279 scale 3 1.5 +fix fxnve all nve + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 500 # time interval for printing out "thermo" data +#thermo_modify flush yes + +#restart 1000000 restart_nvt + +run 500000 + +write_restart system_after_nvt.rst + + diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt new file mode 100644 index 000000000..70fdb7548 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt @@ -0,0 +1,29 @@ +#Define the CNT and CNAD molecules, by including the files which define them +import cnt.lt +import cnad.lt + +# The cnt's center was originally at position 10,10,10, +# so I moved it back to the origin +cnt = new CNT.move(-10,-10,-10) + +# Rotation around the center of mass does not work (yet), +# so instead you have to move the molecule to the origin, +# rotate it, and move it back to where you want it. +# That's why the next line contains move().rot().move() +# I'll add center-of-mass rotation as a later feature. + +cnad1 = new CNAD.move(0.611276,-0.0237931,-0.0487586).rot(90,0,1,0).move(-7,0,0) +cnad2 = new CNAD.move(0.611276,-0.0237931,-0.0487586).rot(-90,0,1,0).move(7,0,0) + + +# You can leave the periodic boundary conditions unspecified +# and change them later, OR you can declare them +# using the "write_once("Data Boundary") {}" command: + +write_once("Data Boundary") +{ + 0 50.0 xlo xhi + 0 50.0 ylo yhi + 0 50.0 zlo zhi +} + diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/README.TXT b/tools/moltemplate/examples/all_atom_examples/hexadecane/README.TXT new file mode 100644 index 000000000..325cc95bd --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/README.TXT @@ -0,0 +1,38 @@ +This example is a simple simulation of 288 hexadecane molecules in a box at +room temperature and atmospheric pressure. Please read the WARNING.TXT file. + +-------- REQUIREMENTS: --------- +This example requires building LAMMPS with the "USER-MISC" package. +(because it uses dihedral_style fourier) +To do this, type "make yes-user-misc" before compiling LAMMPS. + http://lammps.sandia.gov/doc/Section_start.html#start_3 + +More detailed instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files: + +step 1) to setup the LAMMPS input files, run this file: +README_setup.sh + +step 2) to run LAMMPS, follow the instructions in this file: +README_run.sh + +------------ NOTE: There are two versions of this example. ---------------- + +Both examples use the same force-field parameters. + +1) In this directory, all of the force-field parameters are listed explicitly +in the "alkanes.lt" file (located in the "moltemplate_files" directory). +This allows the user to manually control all of the force-field details. + +2) However, there is an alternate version of this example in the +"../AMBER_force_field_examples" directory. +In that version, the force-fields are loaded from a much larger file named +"gaff.lt" which contains all of the parameters in the AMBER GAFF force-field +database. The "gaff.lt" is similar to the "alkanes.lt" file except that +it is larger (because it contains information for nearly all small organic +molecules). It is located in a different directory (in the "common" directory). + +Relying on "gaff.lt" frees the user from the drudgery of manually specifying +all of these force-field details for every molecule. (However, the user must +be careful to choose @atom-type names which match AMBER GAFF conventions, +such as "c3" and "h1", in this example.) diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/README_run.sh b/tools/moltemplate/examples/all_atom_examples/hexadecane/README_run.sh new file mode 100755 index 000000000..8b01ab92d --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/README_run.sh @@ -0,0 +1,39 @@ +# --- Running LAMMPS --- +# -------- REQUIREMENTS: --------- +# 1) This example requires building LAMMPS with the "USER-MISC" package. +# (because it makes use of "gaff.lt" which uses dihedral_style fourier) +# To do this, type "make yes-user-misc" before compiling LAMMPS. +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# -------- PREREQUISITES: -------- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation might be ignored when beginning the simulation at constant +# volume. (This is because restart files in LAMMPS don't always work, +# and I was spending a lot of time trying to convince people it was a +# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) +# Read the "run.in.nvt" file to find out how to use the "read_restart" +# command to load the results of the pressure-equilibration simulation, +# before beginning a constant-volume run. + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/hexadecane/README_setup.sh new file mode 100755 index 000000000..f632ada11 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/README_setup.sh @@ -0,0 +1,25 @@ +# -------- REQUIREMENTS: --------- +# You must define your MOLTEMPLATE_PATH environment variable +# and set it to the "common" subdirectory of your moltemplate distribution. +# (See the "Installation" section in the moltemplate manual.) + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + mv -f system.data system.in* ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + + +cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/hexadecane/README_visualize.txt new file mode 100644 index 000000000..019afc144 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/WARNING.TXT b/tools/moltemplate/examples/all_atom_examples/hexadecane/WARNING.TXT new file mode 100644 index 000000000..def26ba76 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/WARNING.TXT @@ -0,0 +1,16 @@ +# -------- WARNING: -------- + +This software is experimental, and the force-fields and equilbration protocols +have not been tested carefully by me. There is no gaurantee that the simulation +will reproduce the behavior of real hexadecane molecules, +(or even of hexadecane molecules simulated using AMBER, which should + be using the same force-field). + +# -------- REQUEST FOR HELP: -------- + +However, if you notice a problem with this example, please report it. +I confess I do not have a lot of experience running all-atom simulations. +Peer-review is the only way to improve this software (or any software). +Other suggestions are also welcome! + +(Contact jewett.aij@gmail.com, 2013-10-16) diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg b/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg new file mode 100644 index 000000000..b0d31f884 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg b/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg new file mode 100644 index 000000000..f7c13d098 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_LR.jpg b/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_LR.jpg new file mode 100644 index 000000000..3ad353dbb Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/alkanes.lt b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/alkanes.lt new file mode 100644 index 000000000..5b6642b04 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/alkanes.lt @@ -0,0 +1,84 @@ + +Alkanes { + + # LAMMPS offers many different force-field styles and atom-styles. + # We must select which kind of atoms and force fields we want to use. + # (This will effect the syntax of the "_coeff" commands below.) + + write_once("In Init") { + # Default styles and settings for AMBER based force-fields: + units real + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid fourier + #improper_style hybrid cvff + + pair_style hybrid lj/cut 9.0 + pair_modify shift yes + + # If you have charges on the atoms, then comment out the line above + # and use this instead: + #pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + #kspace_style pppm 0.0001 + + pair_modify mix arithmetic + special_bonds amber + } + + # The "Alkanes" object contains the definition of atoms, bonds, bond-angles, + # and all of the force-field parameters for simple n-Alkanes. + # (These parameters were taken from the January 2013 version of the + # AMBER GAFF force-field. See "common/gaff.lt" for details.) + + # atom-type mass + + write_once("Data Masses") { + @atom:c3 12.01 + @atom:h1 1.008 + } + + # Pairwise (non-bonded) force-field parameters: + + write_once("In Settings") { + pair_coeff @atom:c3 @atom:c3 lj/cut 0.1094 1.9080 + pair_coeff @atom:h1 @atom:h1 lj/cut 0.0157 1.3870 + } + + # Rules for determining 3 and 4-body bonded interactions by type + + # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 + + write_once("Data Angles By Type") { + @angle:CCC @atom:c3 @atom:c3 @atom:c3 @bond:* @bond:* + @angle:CCH @atom:c3 @atom:c3 @atom:h1 @bond:* @bond:* + @angle:HCH @atom:h1 @atom:c3 @atom:h1 @bond:* @bond:* + } + + # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3 + + write_once("Data Dihedrals By Type") { + @dihedral:XCCX @atom:* @atom:c3 @atom:c3 @atom:* @bond:* @bond:* @bond:* + @dihedral:CCCC @atom:c3 @atom:c3 @atom:c3 @atom:c3 @bond:* @bond:* @bond:* + } + + # Parameters for these new angular interactions must be defined. (I recommend + # putting all force-field parameters (coeffs) in the "In Settings" section.) + + write_once("In Settings") { + + # bond-type k r0 + bond_coeff @bond:CC harmonic 303.1 1.5350 + bond_coeff @bond:CH harmonic 335.9 1.0930 + + # angle-type k theta0 + angle_coeff @angle:CCC harmonic 63.210 110.630 + angle_coeff @angle:CCH harmonic 46.360 110.070 + angle_coeff @angle:HCH harmonic 39.180 109.550 + + # dihedral-type + dihedral_coeff @dihedral:XCCX fourier 1 0.155555555556 3 0.0 + dihedral_coeff @dihedral:CCCC fourier 3 0.18 3 0.0 0.25 2 180.0 0.2 1 180.0 + } + +} # Alkanes diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch2group.lt new file mode 100644 index 000000000..33051a0c1 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch2group.lt @@ -0,0 +1,44 @@ + +import "alkanes.lt" # <-- Defines the atoms and force-field used for Alkanes + + +CH2 inherits Alkanes { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c3 0.00 0.00 0.000 0.000 + $atom:H1 $mol:... @atom:h1 0.00 0.00 0.6310438442242609 0.8924307629540046 + $atom:H2 $mol:... @atom:h1 0.00 0.00 0.6310438442242609 -0.8924307629540046 + } + + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # parent object's molecule id number as it's own. + # The CH2 group is part of the Hexadecane molecule. + + # Now specify which pairs of atoms are bonded: + # bond-id bond-type atom-id1 atom-id2 + + write('Data Bonds') { + $bond:b1 @bond:CH $atom:C $atom:H1 + $bond:b2 @bond:CH $atom:C $atom:H2 + } + +} # CH2 + + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 + + diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch3group.lt new file mode 100644 index 000000000..b78d9947f --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch3group.lt @@ -0,0 +1,44 @@ + +import "alkanes.lt" # <-- Defines the atoms and force-field used for Alkanes + + +CH3 inherits Alkanes { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c3 0.00 0.00 0.000 0.000 + $atom:H1 $mol:... @atom:h1 0.00 0.00 0.6310438442242609 0.8924307629540046 + $atom:H2 $mol:... @atom:h1 0.00 0.00 0.6310438442242609 -0.8924307629540046 + $atom:H3 $mol:... @atom:h1 0.00 -0.8924307629540046 -0.6310438442242609 0.00 + } + + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # parent object's molecule id number as it's own. + # The CH3 group is part of the Hexadecane molecule. + + # Now specify which pairs of atoms are bonded: + # bond-id bond-type atom-id1 atom-id2 + + write('Data Bonds') { + $bond:b1 @bond:CH $atom:C $atom:H1 + $bond:b2 @bond:CH $atom:C $atom:H2 + $bond:b3 @bond:CH $atom:C $atom:H3 + } + +} # CH3 + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 + diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/hexadecane.lt b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/hexadecane.lt new file mode 100644 index 000000000..c6af2a7a7 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/hexadecane.lt @@ -0,0 +1,84 @@ +# Define the "CH2" and "CH3" objects: + +import "ch2group.lt" +import "ch3group.lt" + + + +Hexadecane inherits Alkanes { + + # Create an array of 16 "CH2" objects + + monomers = new CH2.move(0,0.4431163,0) [16].rot(180,1,0,0).move(1.2533223,0,0) + + # "monomers" is a 1-dimensional array containing 16 copies of the CH2 molecule + # Each copy is rotated 180 degrees and shifted along the x axix. + # (For an explanation, read sections 7.1-7.3 of the moltemplate manual.) + # Notes: + # 1.2533223 = DeltaXc = how far each CH2 group is shifted along the axis + # 0.4431163 = DeltaYc/2 = lateral displacement of carbons along axis + + # ---- Now, modify the ends: --- + # Delete the CH2 groups at the beginning and end, and replace them with CH3. + # (Note: Alternately, instead of deleting the CH2 groups at each end, you + # could modify them by adding an extra hydrogen atom to those carbons.) + + delete monomers[0] + delete monomers[15] + monomer_begin = new CH3 + monomer_end = new CH3 + + # Move the CH3 groups to the correct location at either end of the chain: + + monomer_begin.move(0,0.4431163,0) + monomer_end.move(0,0.4431163,0).rot(180,0,0,1).move(18.7998345,0,0) + + # Note: 18.7998345 = (16-1) * DeltaXc + + + # Now add a list of bonds connecting the carbon atoms together: + + write('Data Bonds') { + $bond:b1 @bond:CC $atom:monomer_begin/C $atom:monomers[1]/C + $bond:b2 @bond:CC $atom:monomers[1]/C $atom:monomers[2]/C + $bond:b3 @bond:CC $atom:monomers[2]/C $atom:monomers[3]/C + $bond:b4 @bond:CC $atom:monomers[3]/C $atom:monomers[4]/C + $bond:b5 @bond:CC $atom:monomers[4]/C $atom:monomers[5]/C + $bond:b6 @bond:CC $atom:monomers[5]/C $atom:monomers[6]/C + $bond:b7 @bond:CC $atom:monomers[6]/C $atom:monomers[7]/C + $bond:b8 @bond:CC $atom:monomers[7]/C $atom:monomers[8]/C + $bond:b9 @bond:CC $atom:monomers[8]/C $atom:monomers[9]/C + $bond:b10 @bond:CC $atom:monomers[9]/C $atom:monomers[10]/C + $bond:b11 @bond:CC $atom:monomers[10]/C $atom:monomers[11]/C + $bond:b12 @bond:CC $atom:monomers[11]/C $atom:monomers[12]/C + $bond:b13 @bond:CC $atom:monomers[12]/C $atom:monomers[13]/C + $bond:b14 @bond:CC $atom:monomers[13]/C $atom:monomers[14]/C + $bond:b15 @bond:CC $atom:monomers[14]/C $atom:monomer_end/C + } + + create_var { $mol } # Define a molecule ID number for this polymer + + # This causes monomer[0], monomer[1], ... to share the same molecule-ID. + # (because in the ch2group.lt file, the "..." in "$mol:..." looks for + # a counter of type "$mol" in a parent molecule or earlier ancestor.) + +} # Hexadecane + + + + + + + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/system.lt new file mode 100644 index 000000000..4e0cfaec6 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/system.lt @@ -0,0 +1,18 @@ +import "hexadecane.lt" # <- defines the "Hexadecane" molecule type. + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 62.4 xlo xhi + 0.0 62.4 ylo yhi + 0.0 62.4 zlo zhi +} + +molecules = new Hexadecane [12].move(0, 0, 5.2) + [12].move(0, 5.2, 0) + [2].move(31.2, 0, 0) + + +# NOTE: The spacing between molecules is large. There should be extra room to +# move during the initial stages of equilibration. However, you will have to +# run the simulation at NPT conditions later to compress the system to a +# more realistic density. diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.npt b/tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.npt new file mode 100644 index 000000000..b1791c955 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.npt @@ -0,0 +1,85 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + +# To avvoid explosions, I have a 4-step equilibraion process (expand, minimize, +# reorient, compress). The system (as defined in the "system.data" file) +# is already expanded. That means there are 3 steps left: + +dump dumpeq1 all custom 50 traj_eq1_min.lammpstrj id mol type x y z ix iy iz +thermo 50 + +# -- Equilibration: part 1: initial minimization -- + +# Note: In general, it's always a good idea to minimize the system at first. + +minimize 1.0e-5 1.0e-7 100000 400000 +undump dumpeq1 + +write_data system_after_eq1_min.data + +# -- Equilibration part 2: reorienting the molecules (NVT) -- + +timestep 1.0 +dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy iz + +# Run the system at high temperature (at constant volume) to reorient the +# the molecules (which would otherwise be pointing in the same direction). + +# To speed it up, I randomize the atomic positions for a few thousand steps +# using fix langevin (and fix nve). Then I switch to fix nvt (Nose-Hoover). +# (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.) + + +fix fxlan all langevin 900.0 900.0 120 48279 +fix fxnve all nve + +run 2000 + +unfix fxlan +unfix fxnve +# Now continue the simulation at high temperature using fix nvt (Nose-Hoover). +fix fxnvt all nvt temp 900.0 900.0 100.0 + +run 5000 +undump dumpeq2 + + +write_data system_after_eq2_reorient.data + +unfix fxnvt + +# -- equilibration part 3: Equilibrating the density (NPT) -- + +# Originally, the simulation box (in "system.data" and "system.lt") was +# unrealistically large. The spacing between the molecules was large also. +# I did this to enable the molecules to move freely and reorient themselves. +# After doing that, we should run the simulation under NPT conditions to +# allow the simulation box to contract to it's natural size. We do that here: +# We begin the simulation at 100 barr (a relatively low pressure), and +# slowly decrease it to 1 barr, maintianing the temperature at 300K. + +dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 300.0 300.0 100.0 iso 100.0 1.0 1000.0 drag 2.0 + +timestep 1.0 +run 30000 + +write_data system_after_eq3_npt.data + diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.nvt new file mode 100644 index 000000000..f8b2d31d0 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.nvt @@ -0,0 +1,42 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_eq3_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 350.0 350.0 500.0 tchain 1 +thermo 100 +#thermo_modify flush yes + +run 50000 + +write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_run.sh b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_run.sh new file mode 100755 index 000000000..cf51fa870 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_run.sh @@ -0,0 +1,33 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure + +# or + +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation are ignored when beginning the simulation at constant volume. +# This can be fixed. Read "run.in.nvt" for equilibration instructions.) + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +# or +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_setup.sh new file mode 100755 index 000000000..3a0821269 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -atomstyle full system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_visualize.txt new file mode 100644 index 000000000..73358e55d --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 500 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg b/tools/moltemplate/examples/all_atom_examples/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg new file mode 100644 index 000000000..2cdc08b31 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce.lt new file mode 100644 index 000000000..2b550b630 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce.lt @@ -0,0 +1,52 @@ +# file "spce.lt" +# +# H1 H2 +# \ / +# O + +SPCE { + + write_once("In Init") { + # -- Default styles (for solo "SPCE" water) -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 + $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 + } + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 1000.0 1.0 + angle_coeff @angle:HOH harmonic 1000.0 109.47 + pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + group spce type @atom:O @atom:H + fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fSHAKE during minimization.) + } + +} # end of definition of "SPCE" water molecule type + diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce_ice_rect8.lt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce_ice_rect8.lt new file mode 100644 index 000000000..ccfd2f18c --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce_ice_rect8.lt @@ -0,0 +1,57 @@ +# This ice (1h) unit cell is rectangular and contains 8 water molecules. +# (Coordinates and cell dimensions converted were from a PDB file.) +# The dimensions of the unit cell (in Angstroms) are: 4.521 7.832 7.362 + + +import "spce.lt" # <-- define the "SPCE" molecule + +SpceIceRect8 { + + # Create a 3-dimensional array of 8 water molecules + + wat = new SPCE[2][2][2] + + # Array indices will be correlated with position [xindex][yindex][zindex] + + # You can overwrite coordinates of atoms after they were created this way: + # (Order is not important) + # atom-ID molecule-ID atomType charge newX newY newZ + + write("Data Atoms") { + $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381 + $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 0.370 1.710 + $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.710 + $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981 + $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 1.305 6.970 + $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.652 + $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300 + $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 2.611 3.289 + $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.320 2.143 1.971 + $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061 + $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.143 5.391 + $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 3.546 5.391 + $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381 + $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 4.286 1.710 + $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 0.320 5.688 1.710 + $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981 + $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 5.221 6.970 + $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.940 5.688 5.652 + $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300 + $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.289 + $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 2.582 6.058 1.971 + $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061 + $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 4.200 6.058 5.391 + $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.462 5.391 + } +} # IceRect8 + +# Credit goes to Martin Chaplin. +# These coordinates were orignally downloaded from Martin Chaplin's +# website: http://www.btinternet.com/~martin.chaplin/ice1h.html +# ... and then they were stretched independently in the xy and z +# directions in order to match the lattice parameters measured by +# Rottger et al., +# "Lattice constants and thermal expansion of H2O and D2O ice Ih" +# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648 +# I am using the lattice constants measured at temperature 265K +# (and pressure=100Torr). diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/system.lt new file mode 100644 index 000000000..b4f22f9dc --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/system.lt @@ -0,0 +1,11 @@ +import "spce_ice_rect8.lt" + +cells = new SpceIceRect8 [3].move(4.521, 0.0, 0.0) + [2].move( 0.0, 7.832, 0.0) + [2].move( 0.0, 0.0, 7.362) + +write_once("Data Boundary") { + 0 13.563 xlo xhi + 0 15.664 ylo yhi + 0 14.724 zlo zhi +} diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.npt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.npt new file mode 100644 index 000000000..2bf2e0c03 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.npt @@ -0,0 +1,38 @@ +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- + +# Note: The minimization step is not necessary in this example. However +# in general, it's always a good idea to minimize the system beforehand. +# fSHAKE was defined in system.in.settings. It is incompatible with "minimize". +unfix fSHAKE +minimize 1.0e-5 1.0e-7 100000 400000 +# Now read "system.in.settings" in order to redefine fSHAKE again: +include system.in.settings + +# -- simulation protocol -- + + +timestep 2.0 +dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 400.0 400.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 + +thermo 100 +#thermo_modify flush yes + +run 20000 + +write_restart system_after_npt.rst diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.nvt new file mode 100644 index 000000000..b23a288c4 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.nvt @@ -0,0 +1,61 @@ +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Normally, I would minimize the system and equilibrate the system at constant +# pressure and temperature beforehand. If you run lammps with "run.in.npt", +# it will generate a restart file "system_after_npt.rst" with reasonable +# coordinates at that temperature and pressure. Then we could load it now: +# +#read_restart system_after_npt.rst +# +# Unfortunately the LAMMPS "read_restart" command has been undependable over +# the past year (2012), and I feel it is safer to remove it from the examples. +# Instead, for this example, I just read the raw coordinates generated by +# moltemplate (and the default volume). (I get fewer questions this way.) +# However you should never run any liquid simulations at constant volume without +# pressure equilibration first. Hopefully in the future "read_restart" will +# work. Until then, try "read_dump", "dump2data.py", or "restart2data". + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- + +# Note: The minimization step is not necessary in this example. However +# in general, it's always a good idea to minimize the system beforehand. +# fSHAKE was defined in system.in.settings. It is incompatible with "minimize". +unfix fSHAKE +minimize 1.0e-5 1.0e-7 100000 400000 +# Now read "system.in.settings" in order to redefine fSHAKE again: +include system.in.settings + +# -- simulation protocol -- + + + +timestep 2.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 + + +thermo 500 +#thermo_modify flush yes + + +#restart 100000 restart_nvt + +run 50000 + +write_restart system_after_nvt.rst + + diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README.TXT b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README.TXT new file mode 100644 index 000000000..83b4ad80b --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README.TXT @@ -0,0 +1,51 @@ +This is a small version of a carbon-nanotube, water capillary system. +It was inspired by this paper: + + Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) + +-------- Requirements: ------- +To run this system at constant pressure, it might help to compile LAMMPS +with the optional RIGID package, and use "fix rigid" on the carbon. +(The use of fix rigid is controversial.) Running at NVT does not require this. +------------------------------ + +Note: To investigate the behavior from that paper, it might be a good + idea to increase the size of the water reservoir, the spacing between + the walls, and the size of the system in the X and Y directions. + +Note: Explicit carbon-carbon bonds: + In the graphene and nanotube structures, I did not try to connect the + carbon atoms together with bonds. Instead we will hold these structures + rigid by not integrating their equations of motion. + (If you want to simulate movement of the carbon atoms at high + temperatures or tension, LAMMPS has 3-body/many-body LAMMPS force-fields + available for simulating the behaviour of carbon in graphite. I know + that you don't need to specify bonds to use these force fields. I do + not know know if these force fields work for nanotubes or graphene.) + +Note: Other modeling tools: + If you need explicit bonds between carbon atoms, then you must add them + yourself or use a different tool. Currently (2012-10-20), moltemplate does + not generate bonds automatically. The "Nanotube Builder" and "topotools" + plugins for for VMD can generate a nanotube with bonds in LAMMPS data + format. You can then convert this data file to .LT format using the + ltemplify.py utility and then import it into another .LT file and play + with it later. (In the "cnad-cnt" example, the carbon nanotube was built + using "Nanotube Builder" and topotools, and processed with ltemplify.py) + + +# WARNING: THIS IS NOT A REALISTIC MODEL OF A GRAPHENE-NANOTUBE JUNCTION. +# A real junction would be curved and deformed near the boundary, +# (not 90 degrees) and it would not be built entirely from hexagons. +# (This is not a problem in this example because the carbon atoms +# are immobilized.) If you want to simulate the behavior of +# real graphene or nanotube junctions, you must be more careful. +# To solve this problem: +# Moltemplate allows you to move, customize or delete individual +# atoms near the boundary. You can move atoms by overwriting their +# coordinates using additional write("Data Atoms") statements (after +# the walls and tube are created). You can also change their charge. +# Alternately, you could start with the structure provided here, and +# relax/minimize the coordinates of the carbon atoms using LAMMPS +# before using it in other simulations. +# Or you could do both (customization & minimization). diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_run.sh b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_run.sh new file mode 100755 index 000000000..8a470b955 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_run.sh @@ -0,0 +1,24 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.nvt # minimization and simulation at constant volume +lmp_linux -i run.in.npt # minimization and simulation at constant pressure + # (WARNING: The "run.in.npt" example has not been + # rigorously tested and may fail.) + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_setup.sh new file mode 100755 index 000000000..acc5fbbaa --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_visualize.txt new file mode 100644 index 000000000..206db9903 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_visualize.txt @@ -0,0 +1,77 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + To shift the box by a fraction in the x direction (for example) + do this: + + pbc wrap -compound res -all -shiftcenterrel {-0.50 -0.52 0.0 } + pbc box -shiftcenterrel {-0.50 -0.52 0.0 } + + # Alternately if you have a solute whose atoms are all of type 1, + # then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 000000000..bf019b4c3 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,3195 @@ +PSF + + 1 !NTITLE + REMARKS VMD-generated NAMD/X-Plor PSF structure file + + 2454 !NATOM + 1 1 1 1 0.000000 12.0000 0 + 2 1 1 1 0.000000 12.0000 0 + 3 2 1 1 0.000000 12.0000 0 + 4 2 1 1 0.000000 12.0000 0 + 5 3 1 1 0.000000 12.0000 0 + 6 3 1 1 0.000000 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b/tools/moltemplate/examples/all_atom_examples/nanotube+water/images/water_side_nopbc_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/README.sh b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/README.sh new file mode 100644 index 000000000..8b16c87e3 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/README.sh @@ -0,0 +1,27 @@ +# This is a small version of a carbon-nanotube, water capillary system. +# It was inspired by this paper: +# +# Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) +# +# Note: To investigate the behavior from that paper, you would have to increase +# the spacing between the two graphene sheets to prevent the water from +# making contact with the lower graphene wall. +# +# Requirements: 1) Set your $MOLTEMPLATE_PATH variable +# 2) The "RIGID" LAMMPS package may be needed later +# To run this system at constant pressure, it might help to compile LAMMPS with +# the optional RIGID package, and use "fix rigid" on the carbon. (Optional.) +# +# Also, if you have not yet done this set your MOLTEMPLATE_PATH environment +# variable to access it. (See installation instructions.) +# Most likely some of the files in this example (like graphene.lt, tip3p2004.lt) +# are not in this directory, but are in the "common" directory. +# Set MOLTEMPLATE_PATH to point to the "common" directory. +# +# ----------------------------------------------------------- +# +# To run moltemplate, use: + +moltemplate.sh system.lt + +# This will generate:system.data, system.in, system.in.init, system.in.settings diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt new file mode 100644 index 000000000..949e16e6b --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt @@ -0,0 +1,119 @@ +# This file contains a unit cell for building graphene and nanotubes +# +# +# The 2AtomCellAlignX "molecule" defined below is a minimal unit cell for any +# hexagonal tesselation in 2-dimensions. (See "graphene_unit_cell.jpg") +# Surfaces constructed with this unit cell can be flat or curved into tubes. +# The distance between nearest-neighbor carbon atoms (ie the length of a +# carbon-carbon bond) is equal to "d" which I set to 1.42 Angstroms. +# +# d = length of each hexagon's side = 1.42 Angstroms +# L = length of each hexagon = 2*d = 2.84 Angstroms +# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478056 Angstroms +# w = width of hexagon rows = 1.5*d = 2.13 Angstroms +# +# Consequently, the Lattice-cell vectors for singe-layer graphene are: +# (2.4595121467478, 0, 0) (aligned with X axis) +# (1.2297560733739, 2.13, 0) (2.13 = 1.5*d) +# So, to build a sheet of graphite, you could use: +# sheet = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) + + + + +Graphene { + + 2AtomCellAlignX + { + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0 + $atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0 + } + } + + # Now define properties of the Carbon graphene atom + + write_once("In Init") { + # If all of the graphene carbon atoms have zero charge, try this: + pair_style hybrid lj/cut 10.0 + + # If some of the boundary atoms have non-zero (partial) charge, try these: + #pair_style hybrid lj/charmm/coul/charmm 9.0 10.0 + #pair_style hybrid lj/charmm/coul/long 9.0 10.0 + } + + write_once("Data Masses") { + @atom:C 12.0 + } + + write_once("In Settings") { + # If all graphene carbon atoms have zero charge, try this: + pair_coeff @atom:C @atom:C lj/cut 0.068443 3.407 + + # i j epsilon sigma + # If some of the boundary atoms have non-zero (partial) charge, try these: + #pair_coeff @atom:C @atom:C lj/charmm/coul/charmm 0.068443 3.407 + #pair_coeff @atom:C @atom:C lj/charmm/coul/long 0.068443 3.407 + + # These Lennard-Jones parameters come from + # R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus, + # Chem Phys Lett, 348:187 (2001) + # LAMMPS provides more realistic manybody force fields for graphene. + # But in this example, we immobilize the atoms so it does not matter.) + + # Define a group consisting of only carbon atoms in graphene molecules + group Cgraphene type @atom:C + } + + # Notice that the two atoms in the unit-cell above lie in the XY plane. + # (Their z-coordinate is zero). It's also useful to have a version of + # this object which lies in the XZ plan. So we define this below: + + 2AtomCellAlignXZ = 2AtomCellAlignX.rot(90,1,0,0) + +} # Graphene + + + + + + + + + + +# ------------ Graphite ----------- +# +# Note: For graphite: sheets stacked in the Z direction are separated by a +# distance of 3.35 Angstroms, and shifted in an alternating +/-Y direction +# by a distance of d (1.42 Angstroms). To add additional graphene layers +# you could use: +# sheet2 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) +# sheet2[*][*].move(0, 1.42, 3.35) +# sheet3 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) +# sheet3[*][*].move(0, -1.42, 6.70) +# etc... +# However, to build a thick sheet of graphite, it would +# be more efficient to use a 4-atom unit cell: +# +#Graphene { +# GraphiteCell { +# # atomID molID atomType charge x y z +# write("Data Atoms") { +# $atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0 +# $atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0 +# $atom:C3 $mol:... @atom:../C 0.0 -0.61487803668695 1.065 3.35 +# $atom:C4 $mol:... @atom:../C 0.0 0.61487803668695 1.775 3.35 +# } +# } # GraphiteCell +#} +# +# Then you could create a thick sheet of graphite this way: +# +# graphite = new Graphene/GraphiteCell [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) +# [5].move(0,0,6.70) diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene_walls.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene_walls.lt new file mode 100644 index 000000000..53499334d --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene_walls.lt @@ -0,0 +1,54 @@ + +import "graphene.lt" + +# -------------- graphene sheet ----------------- + +# Notes: +# Hexagonal lattice with: +# d = length of each hexagonal side = 1.42 Angstroms +# L = length of each hexagon = 2*d = 2.84 Angstroms +# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478 Angstroms +# w = width of hexagon rows = 1.5*d = 2.13 Angstroms + +Wall { + unitcells = new Graphene/2AtomCellAlignX [14].move(1.2297560733739, 2.13, 0) + [13].move(2.4595121467478, 0, 0) + unitcells[*][*].move(-24.595121467478, -14.91, 0.000) + + # Now cut a hole in the graphene sheet roughly where the nanotube is located + delete unitcells[5][7-8] # delete 2 unit cells (2 atoms each, 4 atoms total) + delete unitcells[6][6-8] # delete 3 unit cells (2 atoms each, 6 atoms total) + delete unitcells[7][5-8] # delete 4 unit cells (2 atoms each, 8 atoms total) + delete unitcells[8][5-7] # delete 3 unit cells (2 atoms each, 6 atoms total) + delete unitcells[9][5-6] # delete 2 unit cells (2 atoms each, 4 atoms total) + # Optional fine tuning: delete a few additional atoms around the edges + delete unitcells[5][6]/C2 # delete a single atom + delete unitcells[6][5]/C2 # delete a single atom + delete unitcells[6][9]/C1 # delete a single atom + delete unitcells[8][4]/C2 # delete a single atom + delete unitcells[8][8]/C1 # delete a single atom + delete unitcells[9][7]/C1 # delete a single atom +} + +# Make two copies of the wall, and place them on either end of the nanotube + +wall1 = new Wall.move(0, 0, 32.0) +wall2 = new Wall.move(0, 0, 58.26) + + +# WARNING: A reader has emailed me to point out that: +# THIS IS NOT A REALISTIC MODEL OF A GRAPHENE-NANOTUBE JUNCTION. +# A real junction would be curved and deformed near the boundary, +# (not 90 degrees) and it would not be built entirely from hexagons. +# (This is not a problem in this example because the carbon atoms +# are immobilized.) If you want to simulate the behavior of +# real graphene or nanotube junctions, you must be more careful. +# To solve this problem: +# Moltemplate allows you to move, customize or delete individual +# atoms near the boundary. You can move atoms by overwriting their +# coordinates using additional write("Data Atoms") statements (after +# the walls and tube are created). You can also change their charge. +# Alternately, you could start with the structure provided here, and +# relax/minimize the coordinates of the carbon atoms using LAMMPS +# before using it in other simulations. +# Or you could do both (customization & minimization). diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt new file mode 100644 index 000000000..ee6786d7c --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt @@ -0,0 +1,96 @@ +import "graphene.lt" + +# ------------------ nanotube --------------- + +# Now use this to build a simple ("zigzag") nanotube where the long-axis of each +# hexagon is aligned with the tube axis (along the Z direction). If the +# cicumference of a "zigzag" nanotube contains N hexagons, then the radius of +# the tube, R=(W/4)/tan((2*pi)/(4*N)), where W=2*d*sqrt(3)/2, and d = the carbon +# bond length. If N=14 and d=1.42 Ansgroms then R=5.457193512764 Angstroms +# In the Joly 2011 paper, the tube radii varied between 5.14 and 18.7 Angstroms. + + + + +nanotube = new Graphene/2AtomCellAlignXZ.move(0, 5.457193512764, 0) # 5.45 = R + [14].rot(25.7142857,0,0,1) #25.7=360/14 + [12].rot(12.8571429,0,0,1).move(0, 0, 2.13) #12.9=180/14 + #2.13= d*1.5 + + + # Note: The length is 12 hexegons, the circumference is + # 14 hexegons (~=25.56 and 34.43 Angstroms, respectively). + + +# Move all of the unit-cells in the nanotube between the two graphene sheets. + +nanotube[*][*].move(0, 0, 33.42) + + + + + +# ---------- BUILDING CHIRAL NANOTUBES USING EXTERNAL SOFTWARE ------------- +# +# The approach shown here works well for "zig-zag" nanotubes. +# Nanotubes with other chiralities are more difficult to make this way +# (because the tube axis is no longer perpendicular to graphene basis vectors). +# For those nanotubes, I recommend using an external program to generate +# a LAMMPS data file for the nanotube. If you want to combine the tube +# with other molecules created by moltemplate, you can then import it into +# moltemplate as a molecule object using the "ltemplify.py" utility. Details: +# +# --- VMD plugins (by Axel Kohlmeyer and Robert R. Johnson) --- +# +# The nanotube-builder for VMD can generate nanotubes (with smooth tips) +# for any chirality. These tubes also have explicit bonds between carbons: +# http://www.ks.uiuc.edu/Research/vmd/plugins/nanotube/ +# +# The resulting nanotube can be converted to a data file using topotools: +# https://sites.google.com/site/akohlmey/software/topotools +# To do that, select the "Extensions"->"Tk Console" menu and enter +# +# topo writelammpsdata nanotube.data full +# +# --- ltemplify.py --- +# +# That data file can be converted to moltemplate format (an .LT file) +# using the "ltemplify.py" utility. +# +# The first step is to create a short input script containing the atom_style +# command (ltemplify.py will read this script. Presumably atom_style is "full"). +# +# echo "atom_style full" > nanotube.in +# +# Then run ltemplify to convert nanotube.data into a moltemplate file: +# ltemplify.py -name Nanotube nanotube.in nanotube.data > nanotube.lt +# +# You will need to edit the "nanotuble.lt" file to replace all of the +# "@atom:type1" atoms types file to match the carbon atom types in the other lt +# files (ie "@atom:../C"). If you don't plan on defining bonded interactions +# between carbon atoms, then be sure to remove the write("Data Bonds") section +# of the "nanotube.lt" file (if it is present). +# +# Finally make sure the "system.lt" contains these lines: +# +# import "nanotube.lt" +# nanotube = new Nanotube.move(?,?,?) +# +# (Replace ?,?,? with the location where you want the nanotube to go. +# You can also rotate it using .rot(angle,axisx,axisy,axiz).) +# +# ... and then run moltemplate the normal way +# +# Let me know if you run into trouble with this approach, +# and I will make note of that in this file. +# +# --- links --- +# Note: there are numerous programs for specifying the coordinates +# of the atoms in a nanotube, some of which are below. +# http://www.nanotube.msu.edu/tubeASP/ +# http://turin.nss.udel.edu/research/tubegenonline.html +# http://www.ugr.es/~gmdm/java/contub/contub.html +# (You can load coordinates into moltemplate using the "-xyz" or "-pdb" +# arguments. However currently (2013-12-01), the file must contain coordinates +# for all of the atoms in your sytem, not just the nanotube.) +# ------------------------------------------------------------------------- diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/spce.lt new file mode 100644 index 000000000..019911c19 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/spce.lt @@ -0,0 +1,52 @@ +# file "spce.lt" +# +# H1 H2 +# \ / +# O + +SPCE { + + write_once("In Init") { + # -- Default styles (for solo "SPCE" water) -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 + $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 + } + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 1000.0 1.0 + angle_coeff @angle:HOH harmonic 1000.0 109.47 + pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + group spce type @atom:O @atom:H + fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fShakeSPCE during minimization.) + } + +} # end of definition of "SPCE" water molecule type + diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/system.lt new file mode 100644 index 000000000..e8a9b1bbc --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/system.lt @@ -0,0 +1,46 @@ +# This is a small version of a carbon-nanotube, water capillary system. It was +# inspired by this paper: Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) + +import "graphene_walls.lt" + +import "nanotube.lt" + +import "water_box.lt" + + +# ------------ boundary conditions ------------ + +write_once("Data Boundary") { + -15.98682895386 15.98682895386 xlo xhi + -14.91 14.91 ylo yhi + 0.0 80.00 zlo zhi +} + +# --------------------------------------------- + + + +write_once("In Init") { + # -- override any earlier pair_style settings: -- + # If some of the junction carbon atoms have non-zero partial charge, try this + #pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.5 + + # If all graphened atoms have zero charge, you can use this: + pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.5 & + lj/cut 10.0 + + # I was too lazy to figure out what these partial charges would be, so I set + # them to zero, but a serious investigation into carbon-nanotube-graphene + # junctions would adjust the charge and geometry of the boundary atoms. +} + + +write_once("In Settings") { + # --- We must eventually specify the interactions between the atoms --- + # --- in different molecule types (graphene-water interactions). --- + # (See Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) for details + + pair_coeff @atom:Graphene/C @atom:SPCE/O lj/charmm/coul/long 0.114 3.28 + pair_coeff @atom:Graphene/C @atom:SPCE/H lj/charmm/coul/long 0.0 3.28 +} + diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.lt new file mode 100644 index 000000000..c825276f5 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.lt @@ -0,0 +1,20 @@ +import "spce.lt" + +# --------------- water ------------------ + +# Create a rhombohedral box of water. (A rectangular box works also.) + +wat = new SPCE [9].move(3.5526287, 0, 0 ) + [9].move(1.77631435, 3.3133, 0 ) + [6].move( 0, 0, 3.45) + +# Optional: Center the water box at the origin. (Not really necessary.) + +wat[*][*][*].move(-23.9802437, -14.90985, 11.47) + +# --------------- Note: ----------------- +# The spacing between water molecules does not matter much as long as it is +# reasonable. (I adjusted the spacing try to insure that the waters are spread +# uniformly throughout the box. We do not want bubles to form if there are +# gaps near the XY periodic boundaries.) We will have to equilibrate it later. + diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt new file mode 100644 index 000000000..6bd4fd8a1 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt @@ -0,0 +1,102 @@ +# THIS EXAMPLE HAS NOT BEEN RIGOROUSLY TESTED. +# (This simulation may fail. +# However the "run.in.nvt" example in this directory should work.) +# +# Requirements: +# To run this system at constant pressure, it might help to compile LAMMPS with +# the optional RIGID package, and use "fix rigid" on the carbon. (Optional.) +# The use of fix rigid is controversial. This method is demonstrated below. + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# Only the Cgraphene atoms are immobile. +group mobile subtract all Cgraphene + + +# Unfortunately you can not use the LAMMPS "minimize" command on this system +# because there is no way to immobilize the carbon graphene & nanotube atoms +# during minimization. Instead, we can use langevin dynamics with a large +# damping parameter and a small timestep. + +print "--------- beginning minimization (using fix langevin) ---------" + +timestep 0.1 +fix fxlan mobile langevin 1.0 1.0 100.0 48279 +fix fxnve mobile nve # <-- needed by fix langevin (see lammps documentation) +thermo 100 +run 2500 + +unfix fxlan +unfix fxnve + +# -- simulation protocol -- + +print "--------- beginning simulation (using fix nvt) ---------" + +timestep 0.25 +dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 1000 # time interval for printing out "thermo" data + + + + + +# ------------------------- NPT --------------------------- + +# Set temp=300K, pressure=100bar, and equilibrate volume only in the z direction + +fix fxMoveStuff mobile npt temp 300 300 100 z 100 100 1000.0 dilate mobile + +# ------ QUESTIONABLE (see below): ------ + +fix Ffreezestuff Cgraphene rigid/npt single temp 300 300 100 z 100 100 1000.0 force * off off off torque * off off off dilate mobile + +# -- Alternate npt rigid method -- +# I'm not sure which way is more correct, however +# this also seems to behave in a reasonable-looking way: +#fix Ffreezestuff Cgraphene rigid single force * off off off torque * off off off +# +# The use of either "fix rigid" or "fix rigid/npt" to immobilize +# an object is somewhat controversial. Feel free to omit it. +#(Neither Trung or Steve Plimpton use rigid or rigid/npt for immobilizing +#molecules, but I noticed that at NPT, it does a better job of maintaining +# the correct volume. However "fix rigid" has changed since then (2011), +# so this may no longer be true. Please use this example with caution.) +# ---------------------------------------- + +# IMPORTANT for NPT: You must use "neigh_modify" to turn off calculation of the +# forces between immobilized atoms. +neigh_modify exclude group Cgraphene Cgraphene + +# The next two lines recalculate the temperature +# using only the mobile degrees of freedom: + +compute tempMobile mobile temp +compute pressMobile all pressure tempMobile + +thermo_style custom step c_tempMobile c_pressMobile temp press vol + +fix_modify fxMoveStuff temp tempMobile + +run 100000 + +write_data system_after_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also.) + diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt new file mode 100644 index 000000000..59c847c07 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt @@ -0,0 +1,79 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# (You do not need to run LAMMPS to equilibrate the system before +# using this file.) + +# ----------------------------- Initialization Section -------------------- + +include system.in.init + + +# ----------------------------- Atom Definition Section ------------------- + +read_data system.data + + +# ----------------------------- Settings Section -------------------------- + +include system.in.settings + + +# ----------------------------- Run Section ------------------------------- + + + +# Optional: Improve efficiency by omitting the calcuation of interactions +# between immobile atoms. (Note: This is not optional under NPT conditions.) +neigh_modify exclude group Cgraphene Cgraphene + +# Only the Cgraphene atoms are immobile. +group mobile subtract all Cgraphene + + + +# -- minimization protocol -- + +# Unfortunately you can not use the LAMMPS "minimize" command on this system +# because there is no way to immobilize the carbon graphene & nanotube atoms +# during minimization. Instead, we can use langevin dynamics with a large +# damping parameter and a small timestep. + +print "--------- beginning minimization (using fix langevin) ---------" + +timestep 0.1 +fix fxlan mobile langevin 1.0 1.0 100.0 48279 +fix fxnve mobile nve # <-- needed by fix langevin (see lammps documentation) +thermo 100 +run 2500 + +unfix fxlan +unfix fxnve + +# -- simulation protocol -- + +print "--------- beginning simulation (using fix nvt) ---------" + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz + +thermo_style custom step temp pe etotal press vol epair #ebond eangle edihed +thermo 500 # time interval for printing out "thermo" data + + +# Integrate the equations of motion: +fix fxMoveStuff mobile nvt temp 300.0 300.0 100.0 + +# The next two lines recalculate the temperature +# using only the mobile degrees of freedom: + +compute tempMobile mobile temp +fix_modify fxMoveStuff temp tempMobile + +restart 5000000 restart_nvt +run 10000000 + +write_data system_after_nvt.data + diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT new file mode 100644 index 000000000..0e58ef44c --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT @@ -0,0 +1,10 @@ +This is a simple system of 260 water molecules. + +In this example, the coordinates of the atoms are read from a PDB file +instead of being specified manually (as well as the boundary information). + +The PDB file was generated by the useful "solvate" utility which comes with VMD. +(To generate this file yourself, run VMD, click on the "Extensions" menu, +and select Modeling-->Add Solvation Box. +In this example, I made a box whose x,y,z dimensions were 16,24,24.) + diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh new file mode 100755 index 000000000..022c53ce3 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh @@ -0,0 +1,31 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation are ignored when beginning the simulation at constant volume. +# This can be fixed. Read "run.in.nvt" for equilibration instructions.) + + + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh new file mode 100755 index 000000000..5d2be2133 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh @@ -0,0 +1,32 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + +cd moltemplate_files/ # (The .lt input files are in this directory) + + moltemplate.sh -pdb solvate.pdb system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ + + +# +#This will prepare LAMMPS input files for a box of water +#(In this example, we are using the "SPC/E" water model.) +#The number of water molecules in the "wat = new SPCE [260]" command +#must equal the number of water molecules in the PDB file. +# +#Coordinates and boundary-box information is read from the .pdb file. +# +#You can also specify this information directly in the ttree file. +#See the comments section in "system.lt" for details. +# diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt new file mode 100644 index 000000000..8063d535f --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt @@ -0,0 +1,64 @@ + ------- Instructions to view a trajectory in VMD -------- + + ------- Disclaimer ------- + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + + (Note, at this point the image shown in the VMD graphics window may + not appear correct or incomplete. The coordinates of the atoms may + overlap if you asked moltemplate.sh to load your coordinates from + a PDB or XYZ file. + However, later after you have run a simulation, the trajectories + should appear reasonably correct when you load them in VMD using + the PSF file you just generated.) + + +Later, to Load a trajectory in VMD: + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it + +----- Wrap the coordinates to the unit cell + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Enter: + + DISCLAIMER: I'M NOT SURE THESE COMMANDS ARE CORRECT. + LOOKUP "pbctools" FOR DETAILS. + + pbc wrap -compound res -all + pbc box + + # If you have a solute of type 1, then use this: + #pbc wrap -sel type=1 -all -centersel type=2 -center com + +"1" corresponds to the "O" atom type +"2" corresponds to the "H" atom type + +3) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types: + +sed -e 's/ 1 1 / O O /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > system.psf + +(If you do this, I guess that you might have to use + "type=O" and "type=H" in step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/.0 b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/.0 new file mode 100644 index 000000000..e69de29bb diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh new file mode 100755 index 000000000..4ebc7b17a --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh @@ -0,0 +1,11 @@ + +# Run moltemplate this way: + +moltemplate.sh -pdb solvate.pdb system.lt + + +# The PDB file was generated by the "solvate" utility which comes with VMD. +# (To generate this file yourself, run VMD, click on the "Extensions" menu, +# and select Modeling-->Add Solvation Box. +# In this example, I made a box whose x,y,z dimensions were 16,24,24.) + diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb new file mode 100644 index 000000000..0ed5103cb --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb @@ -0,0 +1,782 @@ +CRYST1 16.000 24.000 24.000 90.00 90.00 90.00 P 1 1 +ATOM 1 OH2 TIP3W 5 3.668 10.082 15.904 1.00 0.00 WT1 O +ATOM 2 H1 TIP3W 5 3.224 10.451 15.101 1.00 0.00 WT1 H +ATOM 3 H2 TIP3W 5 3.092 10.379 16.627 1.00 0.00 WT1 H +ATOM 4 OH2 TIP3W 7 6.033 4.876 20.891 1.00 0.00 WT1 O +ATOM 5 H1 TIP3W 7 6.078 5.224 21.798 1.00 0.00 WT1 H +ATOM 6 H2 TIP3W 7 6.592 4.088 20.961 1.00 0.00 WT1 H +ATOM 7 OH2 TIP3W 21 5.186 16.696 12.072 1.00 0.00 WT1 O +ATOM 8 H1 TIP3W 21 6.083 16.979 11.816 1.00 0.00 WT1 H +ATOM 9 H2 TIP3W 21 5.337 15.832 12.490 1.00 0.00 WT1 H +ATOM 10 OH2 TIP3W 29 8.324 13.811 21.332 1.00 0.00 WT1 O +ATOM 11 H1 TIP3W 29 8.633 13.348 22.112 1.00 0.00 WT1 H +ATOM 12 H2 TIP3W 29 8.506 13.116 20.645 1.00 0.00 WT1 H +ATOM 13 OH2 TIP3W 44 3.786 16.318 1.310 1.00 0.00 WT1 O +ATOM 14 H1 TIP3W 44 3.781 15.388 1.196 1.00 0.00 WT1 H +ATOM 15 H2 TIP3W 44 4.528 16.580 0.781 1.00 0.00 WT1 H +ATOM 16 OH2 TIP3W 46 6.205 6.991 18.442 1.00 0.00 WT1 O +ATOM 17 H1 TIP3W 46 6.782 7.347 19.152 1.00 0.00 WT1 H +ATOM 18 H2 TIP3W 46 5.309 7.062 18.800 1.00 0.00 WT1 H +ATOM 19 OH2 TIP3W 48 2.750 8.844 9.629 1.00 0.00 WT1 O +ATOM 20 H1 TIP3W 48 2.110 8.290 9.998 1.00 0.00 WT1 H +ATOM 21 H2 TIP3W 48 2.164 9.245 8.962 1.00 0.00 WT1 H +ATOM 22 OH2 TIP3W 52 3.935 16.195 22.109 1.00 0.00 WT1 O +ATOM 23 H1 TIP3W 52 4.870 16.034 21.985 1.00 0.00 WT1 H +ATOM 24 H2 TIP3W 52 3.655 15.367 22.581 1.00 0.00 WT1 H +ATOM 25 OH2 TIP3W 64 10.674 8.909 4.986 1.00 0.00 WT1 O +ATOM 26 H1 TIP3W 64 10.998 8.871 5.932 1.00 0.00 WT1 H +ATOM 27 H2 TIP3W 64 9.748 9.270 5.075 1.00 0.00 WT1 H +ATOM 28 OH2 TIP3W 67 0.002 5.667 14.591 1.00 0.00 WT1 O +ATOM 29 H1 TIP3W 67 0.483 5.990 13.830 1.00 0.00 WT1 H +ATOM 30 H2 TIP3W 67 0.608 5.781 15.347 1.00 0.00 WT1 H +ATOM 31 OH2 TIP3W 68 9.882 9.156 14.916 1.00 0.00 WT1 O +ATOM 32 H1 TIP3W 68 9.574 9.753 15.597 1.00 0.00 WT1 H +ATOM 33 H2 TIP3W 68 10.021 8.264 15.289 1.00 0.00 WT1 H +ATOM 34 OH2 TIP3W 87 1.661 6.681 1.943 1.00 0.00 WT1 O +ATOM 35 H1 TIP3W 87 1.943 5.739 1.981 1.00 0.00 WT1 H +ATOM 36 H2 TIP3W 87 0.778 6.599 1.483 1.00 0.00 WT1 H +ATOM 37 OH2 TIP3W 88 4.821 20.603 11.239 1.00 0.00 WT1 O +ATOM 38 H1 TIP3W 88 5.466 20.782 11.963 1.00 0.00 WT1 H +ATOM 39 H2 TIP3W 88 5.384 20.914 10.456 1.00 0.00 WT1 H +ATOM 40 OH2 TIP3W 90 15.022 20.855 12.831 1.00 0.00 WT1 O +ATOM 41 H1 TIP3W 90 14.222 20.809 13.292 1.00 0.00 WT1 H +ATOM 42 H2 TIP3W 90 14.673 21.057 11.918 1.00 0.00 WT1 H +ATOM 43 OH2 TIP3W 94 1.339 3.782 22.814 1.00 0.00 WT1 O +ATOM 44 H1 TIP3W 94 0.839 3.425 22.087 1.00 0.00 WT1 H +ATOM 45 H2 TIP3W 94 1.775 3.077 23.138 1.00 0.00 WT1 H +ATOM 46 OH2 TIP3W 95 0.485 15.137 22.476 1.00 0.00 WT1 O +ATOM 47 H1 TIP3W 95 0.644 15.425 23.349 1.00 0.00 WT1 H +ATOM 48 H2 TIP3W 95 0.312 15.961 21.975 1.00 0.00 WT1 H +ATOM 49 OH2 TIP3W 111 10.426 7.604 2.404 1.00 0.00 WT1 O +ATOM 50 H1 TIP3W 111 10.761 8.401 1.994 1.00 0.00 WT1 H +ATOM 51 H2 TIP3W 111 10.248 7.889 3.308 1.00 0.00 WT1 H +ATOM 52 OH2 TIP3W 113 4.269 22.752 16.265 1.00 0.00 WT1 O +ATOM 53 H1 TIP3W 113 4.149 23.680 15.888 1.00 0.00 WT1 H +ATOM 54 H2 TIP3W 113 5.061 22.796 16.776 1.00 0.00 WT1 H +ATOM 55 OH2 TIP3W 130 10.926 5.365 1.018 1.00 0.00 WT1 O +ATOM 56 H1 TIP3W 130 11.138 4.769 1.754 1.00 0.00 WT1 H +ATOM 57 H2 TIP3W 130 10.657 6.212 1.493 1.00 0.00 WT1 H +ATOM 58 OH2 TIP3W 133 8.647 4.314 19.278 1.00 0.00 WT1 O +ATOM 59 H1 TIP3W 133 7.964 3.611 19.326 1.00 0.00 WT1 H +ATOM 60 H2 TIP3W 133 8.043 5.064 19.153 1.00 0.00 WT1 H +ATOM 61 OH2 TIP3W 134 8.381 17.319 23.275 1.00 0.00 WT1 O +ATOM 62 H1 TIP3W 134 7.516 17.340 23.695 1.00 0.00 WT1 H +ATOM 63 H2 TIP3W 134 8.431 18.263 23.009 1.00 0.00 WT1 H +ATOM 64 OH2 TIP3W 150 4.299 17.774 7.169 1.00 0.00 WT1 O +ATOM 65 H1 TIP3W 150 3.303 17.803 7.322 1.00 0.00 WT1 H +ATOM 66 H2 TIP3W 150 4.533 18.755 6.924 1.00 0.00 WT1 H +ATOM 67 OH2 TIP3W 152 8.892 12.977 5.321 1.00 0.00 WT1 O +ATOM 68 H1 TIP3W 152 8.119 12.478 5.443 1.00 0.00 WT1 H +ATOM 69 H2 TIP3W 152 9.342 12.557 4.536 1.00 0.00 WT1 H +ATOM 70 OH2 TIP3W 167 2.174 18.468 2.212 1.00 0.00 WT1 O +ATOM 71 H1 TIP3W 167 2.632 17.628 2.203 1.00 0.00 WT1 H +ATOM 72 H2 TIP3W 167 2.931 19.120 2.281 1.00 0.00 WT1 H +ATOM 73 OH2 TIP3W 239 13.612 17.680 18.622 1.00 0.00 WT1 O +ATOM 74 H1 TIP3W 239 13.744 17.414 19.508 1.00 0.00 WT1 H +ATOM 75 H2 TIP3W 239 14.526 17.831 18.347 1.00 0.00 WT1 H +ATOM 76 OH2 TIP3W 443 9.935 12.876 10.191 1.00 0.00 WT1 O +ATOM 77 H1 TIP3W 443 9.709 12.098 9.634 1.00 0.00 WT1 H +ATOM 78 H2 TIP3W 443 9.472 12.766 11.018 1.00 0.00 WT1 H +ATOM 79 OH2 TIP3W 450 7.060 2.074 19.830 1.00 0.00 WT1 O +ATOM 80 H1 TIP3W 450 7.650 1.619 20.528 1.00 0.00 WT1 H +ATOM 81 H2 TIP3W 450 6.148 1.796 20.035 1.00 0.00 WT1 H +ATOM 82 OH2 TIP3W 465 13.891 1.919 2.992 1.00 0.00 WT1 O +ATOM 83 H1 TIP3W 465 14.198 2.681 3.422 1.00 0.00 WT1 H +ATOM 84 H2 TIP3W 465 13.212 1.577 3.578 1.00 0.00 WT1 H +ATOM 85 OH2 TIP3W 466 8.823 10.581 8.827 1.00 0.00 WT1 O +ATOM 86 H1 TIP3W 466 8.183 10.753 8.148 1.00 0.00 WT1 H +ATOM 87 H2 TIP3W 466 8.389 10.061 9.534 1.00 0.00 WT1 H +ATOM 88 OH2 TIP3W 469 9.078 11.967 12.734 1.00 0.00 WT1 O +ATOM 89 H1 TIP3W 469 8.228 11.561 12.993 1.00 0.00 WT1 H +ATOM 90 H2 TIP3W 469 9.512 12.194 13.560 1.00 0.00 WT1 H +ATOM 91 OH2 TIP3W 484 10.282 0.640 2.053 1.00 0.00 WT1 O +ATOM 92 H1 TIP3W 484 10.367 0.959 3.016 1.00 0.00 WT1 H +ATOM 93 H2 TIP3W 484 9.743 1.323 1.667 1.00 0.00 WT1 H +ATOM 94 OH2 TIP3W 485 4.618 8.125 7.777 1.00 0.00 WT1 O +ATOM 95 H1 TIP3W 485 5.405 7.919 8.314 1.00 0.00 WT1 H +ATOM 96 H2 TIP3W 485 4.002 8.458 8.422 1.00 0.00 WT1 H +ATOM 97 OH2 TIP3W 486 3.403 4.687 9.815 1.00 0.00 WT1 O +ATOM 98 H1 TIP3W 486 3.109 5.272 9.097 1.00 0.00 WT1 H +ATOM 99 H2 TIP3W 486 3.817 3.973 9.327 1.00 0.00 WT1 H +ATOM 100 OH2 TIP3W 489 3.276 7.465 19.325 1.00 0.00 WT1 O +ATOM 101 H1 TIP3W 489 2.772 6.991 19.964 1.00 0.00 WT1 H +ATOM 102 H2 TIP3W 489 3.604 8.288 19.753 1.00 0.00 WT1 H +ATOM 103 OH2 TIP3W 503 3.119 10.325 13.158 1.00 0.00 WT1 O +ATOM 104 H1 TIP3W 503 3.598 10.900 12.512 1.00 0.00 WT1 H +ATOM 105 H2 TIP3W 503 3.440 9.430 12.962 1.00 0.00 WT1 H +ATOM 106 OH2 TIP3W 506 2.378 5.806 16.253 1.00 0.00 WT1 O +ATOM 107 H1 TIP3W 506 2.157 6.161 17.099 1.00 0.00 WT1 H +ATOM 108 H2 TIP3W 506 3.301 6.032 16.126 1.00 0.00 WT1 H +ATOM 109 OH2 TIP3W 507 6.382 22.271 2.319 1.00 0.00 WT1 O +ATOM 110 H1 TIP3W 507 5.550 22.035 1.847 1.00 0.00 WT1 H +ATOM 111 H2 TIP3W 507 6.859 21.472 2.192 1.00 0.00 WT1 H +ATOM 112 OH2 TIP3W 509 4.017 3.905 19.418 1.00 0.00 WT1 O +ATOM 113 H1 TIP3W 509 3.142 4.042 19.132 1.00 0.00 WT1 H +ATOM 114 H2 TIP3W 509 4.582 4.727 19.295 1.00 0.00 WT1 H +ATOM 115 OH2 TIP3W 511 2.344 20.472 21.631 1.00 0.00 WT1 O +ATOM 116 H1 TIP3W 511 2.932 20.821 20.945 1.00 0.00 WT1 H +ATOM 117 H2 TIP3W 511 1.467 20.548 21.138 1.00 0.00 WT1 H +ATOM 118 OH2 TIP3W 517 14.526 10.532 20.137 1.00 0.00 WT1 O +ATOM 119 H1 TIP3W 517 14.162 9.733 20.503 1.00 0.00 WT1 H +ATOM 120 H2 TIP3W 517 14.466 10.420 19.194 1.00 0.00 WT1 H +ATOM 121 OH2 TIP3W 533 5.573 14.804 19.090 1.00 0.00 WT1 O +ATOM 122 H1 TIP3W 533 5.959 15.339 19.808 1.00 0.00 WT1 H +ATOM 123 H2 TIP3W 533 5.869 15.413 18.331 1.00 0.00 WT1 H +ATOM 124 OH2 TIP3W 543 5.458 13.097 4.589 1.00 0.00 WT1 O +ATOM 125 H1 TIP3W 543 5.673 13.019 3.612 1.00 0.00 WT1 H +ATOM 126 H2 TIP3W 543 4.899 13.894 4.657 1.00 0.00 WT1 H +ATOM 127 OH2 TIP3W 550 4.552 1.370 20.330 1.00 0.00 WT1 O +ATOM 128 H1 TIP3W 550 4.274 2.194 19.953 1.00 0.00 WT1 H +ATOM 129 H2 TIP3W 550 4.235 0.801 19.571 1.00 0.00 WT1 H +ATOM 130 OH2 TIP3W 554 5.160 13.744 7.954 1.00 0.00 WT1 O +ATOM 131 H1 TIP3W 554 6.048 13.422 8.207 1.00 0.00 WT1 H +ATOM 132 H2 TIP3W 554 5.008 14.493 8.528 1.00 0.00 WT1 H +ATOM 133 OH2 TIP3W 558 10.390 6.386 18.828 1.00 0.00 WT1 O +ATOM 134 H1 TIP3W 558 10.688 6.484 19.731 1.00 0.00 WT1 H +ATOM 135 H2 TIP3W 558 9.844 5.589 18.921 1.00 0.00 WT1 H +ATOM 136 OH2 TIP3W 562 1.678 21.942 1.035 1.00 0.00 WT1 O +ATOM 137 H1 TIP3W 562 1.272 21.280 1.592 1.00 0.00 WT1 H +ATOM 138 H2 TIP3W 562 1.498 22.809 1.493 1.00 0.00 WT1 H +ATOM 139 OH2 TIP3W 568 9.630 21.547 3.000 1.00 0.00 WT1 O +ATOM 140 H1 TIP3W 568 9.601 22.471 2.643 1.00 0.00 WT1 H +ATOM 141 H2 TIP3W 568 9.287 20.954 2.312 1.00 0.00 WT1 H +ATOM 142 OH2 TIP3W 575 2.344 10.571 2.624 1.00 0.00 WT1 O +ATOM 143 H1 TIP3W 575 2.122 10.753 3.553 1.00 0.00 WT1 H +ATOM 144 H2 TIP3W 575 2.947 9.791 2.617 1.00 0.00 WT1 H +ATOM 145 OH2 TIP3W 584 0.823 23.668 2.888 1.00 0.00 WT1 O +ATOM 146 H1 TIP3W 584 1.636 23.316 3.340 1.00 0.00 WT1 H +ATOM 147 H2 TIP3W 584 0.253 23.978 3.640 1.00 0.00 WT1 H +ATOM 148 OH2 TIP3W 594 2.710 6.185 7.540 1.00 0.00 WT1 O +ATOM 149 H1 TIP3W 594 2.467 6.236 6.561 1.00 0.00 WT1 H +ATOM 150 H2 TIP3W 594 3.410 6.855 7.580 1.00 0.00 WT1 H +ATOM 151 OH2 TIP3W 595 6.911 19.458 17.335 1.00 0.00 WT1 O +ATOM 152 H1 TIP3W 595 7.517 20.118 16.957 1.00 0.00 WT1 H +ATOM 153 H2 TIP3W 595 6.315 19.136 16.588 1.00 0.00 WT1 H +ATOM 154 OH2 TIP3W 613 13.540 22.220 2.748 1.00 0.00 WT1 O +ATOM 155 H1 TIP3W 613 12.965 22.475 3.462 1.00 0.00 WT1 H +ATOM 156 H2 TIP3W 613 14.428 22.404 3.074 1.00 0.00 WT1 H +ATOM 157 OH2 TIP3W 634 10.929 14.750 5.718 1.00 0.00 WT1 O +ATOM 158 H1 TIP3W 634 10.050 14.541 5.408 1.00 0.00 WT1 H +ATOM 159 H2 TIP3W 634 11.401 13.879 5.717 1.00 0.00 WT1 H +ATOM 160 OH2 TIP3W 822 0.747 4.469 10.579 1.00 0.00 WT1 O +ATOM 161 H1 TIP3W 822 0.426 3.568 10.339 1.00 0.00 WT1 H +ATOM 162 H2 TIP3W 822 1.505 4.585 9.990 1.00 0.00 WT1 H +ATOM 163 OH2 TIP3W 849 5.356 5.388 16.046 1.00 0.00 WT1 O +ATOM 164 H1 TIP3W 849 5.884 6.064 16.461 1.00 0.00 WT1 H +ATOM 165 H2 TIP3W 849 5.592 4.622 16.537 1.00 0.00 WT1 H +ATOM 166 OH2 TIP3W 867 10.704 6.721 15.883 1.00 0.00 WT1 O +ATOM 167 H1 TIP3W 867 10.901 6.912 16.836 1.00 0.00 WT1 H +ATOM 168 H2 TIP3W 867 10.127 5.972 15.998 1.00 0.00 WT1 H +ATOM 169 OH2 TIP3W 891 11.763 19.614 9.958 1.00 0.00 WT1 O +ATOM 170 H1 TIP3W 891 12.279 20.405 9.866 1.00 0.00 WT1 H +ATOM 171 H2 TIP3W 891 12.435 18.905 9.901 1.00 0.00 WT1 H +ATOM 172 OH2 TIP3W 906 7.027 2.224 13.411 1.00 0.00 WT1 O +ATOM 173 H1 TIP3W 906 6.185 2.801 13.535 1.00 0.00 WT1 H +ATOM 174 H2 TIP3W 906 6.692 1.403 13.742 1.00 0.00 WT1 H +ATOM 175 OH2 TIP3W 908 4.028 7.699 12.776 1.00 0.00 WT1 O +ATOM 176 H1 TIP3W 908 4.577 7.193 12.138 1.00 0.00 WT1 H +ATOM 177 H2 TIP3W 908 3.171 7.320 12.544 1.00 0.00 WT1 H +ATOM 178 OH2 TIP3W 924 12.493 9.451 2.215 1.00 0.00 WT1 O +ATOM 179 H1 TIP3W 924 12.908 9.840 2.987 1.00 0.00 WT1 H +ATOM 180 H2 TIP3W 924 12.982 8.641 2.039 1.00 0.00 WT1 H +ATOM 181 OH2 TIP3W 927 11.177 9.610 7.928 1.00 0.00 WT1 O +ATOM 182 H1 TIP3W 927 10.443 10.172 8.053 1.00 0.00 WT1 H +ATOM 183 H2 TIP3W 927 10.866 8.788 8.298 1.00 0.00 WT1 H +ATOM 184 OH2 TIP3W 928 1.838 3.206 15.398 1.00 0.00 WT1 O +ATOM 185 H1 TIP3W 928 2.201 4.081 15.545 1.00 0.00 WT1 H +ATOM 186 H2 TIP3W 928 2.117 2.999 14.422 1.00 0.00 WT1 H +ATOM 187 OH2 TIP3W 930 1.899 11.624 17.893 1.00 0.00 WT1 O +ATOM 188 H1 TIP3W 930 1.139 11.678 17.305 1.00 0.00 WT1 H +ATOM 189 H2 TIP3W 930 2.258 12.535 17.855 1.00 0.00 WT1 H +ATOM 190 OH2 TIP3W 932 9.220 13.904 17.340 1.00 0.00 WT1 O +ATOM 191 H1 TIP3W 932 10.062 14.198 17.738 1.00 0.00 WT1 H +ATOM 192 H2 TIP3W 932 9.394 12.999 17.102 1.00 0.00 WT1 H +ATOM 193 OH2 TIP3W 933 3.458 9.868 22.419 1.00 0.00 WT1 O +ATOM 194 H1 TIP3W 933 4.398 10.016 22.654 1.00 0.00 WT1 H +ATOM 195 H2 TIP3W 933 3.448 10.189 21.495 1.00 0.00 WT1 H +ATOM 196 OH2 TIP3W 947 15.430 3.274 7.407 1.00 0.00 WT1 O +ATOM 197 H1 TIP3W 947 15.458 2.741 8.157 1.00 0.00 WT1 H +ATOM 198 H2 TIP3W 947 15.933 2.740 6.770 1.00 0.00 WT1 H +ATOM 199 OH2 TIP3W 948 13.134 4.535 6.559 1.00 0.00 WT1 O +ATOM 200 H1 TIP3W 948 12.434 3.932 6.938 1.00 0.00 WT1 H +ATOM 201 H2 TIP3W 948 13.959 4.162 6.965 1.00 0.00 WT1 H +ATOM 202 OH2 TIP3W 951 10.295 14.066 14.320 1.00 0.00 WT1 O +ATOM 203 H1 TIP3W 951 10.592 14.067 15.226 1.00 0.00 WT1 H +ATOM 204 H2 TIP3W 951 9.322 14.226 14.350 1.00 0.00 WT1 H +ATOM 205 OH2 TIP3W 964 7.830 19.751 1.995 1.00 0.00 WT1 O +ATOM 206 H1 TIP3W 964 7.257 19.870 1.247 1.00 0.00 WT1 H +ATOM 207 H2 TIP3W 964 8.329 18.923 1.885 1.00 0.00 WT1 H +ATOM 208 OH2 TIP3W 972 15.027 11.249 9.806 1.00 0.00 WT1 O +ATOM 209 H1 TIP3W 972 15.636 10.953 9.104 1.00 0.00 WT1 H +ATOM 210 H2 TIP3W 972 14.929 12.194 9.545 1.00 0.00 WT1 H +ATOM 211 OH2 TIP3W 974 10.274 11.448 20.959 1.00 0.00 WT1 O +ATOM 212 H1 TIP3W 974 10.893 11.073 21.654 1.00 0.00 WT1 H +ATOM 213 H2 TIP3W 974 10.344 10.891 20.238 1.00 0.00 WT1 H +ATOM 214 OH2 TIP3W 975 11.473 6.075 21.702 1.00 0.00 WT1 O +ATOM 215 H1 TIP3W 975 12.046 5.667 22.431 1.00 0.00 WT1 H +ATOM 216 H2 TIP3W 975 10.554 5.939 22.100 1.00 0.00 WT1 H +ATOM 217 OH2 TIP3W 995 6.800 16.659 17.184 1.00 0.00 WT1 O +ATOM 218 H1 TIP3W 995 7.143 16.649 16.327 1.00 0.00 WT1 H +ATOM 219 H2 TIP3W 995 7.109 17.502 17.568 1.00 0.00 WT1 H +ATOM 220 OH2 TIP3W1007 14.603 18.110 3.213 1.00 0.00 WT1 O +ATOM 221 H1 TIP3W1007 14.275 17.655 3.963 1.00 0.00 WT1 H +ATOM 222 H2 TIP3W1007 13.842 18.606 2.878 1.00 0.00 WT1 H +ATOM 223 OH2 TIP3W1011 4.753 20.139 5.475 1.00 0.00 WT1 O +ATOM 224 H1 TIP3W1011 4.769 21.053 5.846 1.00 0.00 WT1 H +ATOM 225 H2 TIP3W1011 5.663 20.031 5.201 1.00 0.00 WT1 H +ATOM 226 OH2 TIP3W1013 1.615 17.355 14.355 1.00 0.00 WT1 O +ATOM 227 H1 TIP3W1013 1.225 16.480 14.420 1.00 0.00 WT1 H +ATOM 228 H2 TIP3W1013 0.859 17.984 14.051 1.00 0.00 WT1 H +ATOM 229 OH2 TIP3W1014 11.087 15.787 20.150 1.00 0.00 WT1 O +ATOM 230 H1 TIP3W1014 11.221 14.877 19.698 1.00 0.00 WT1 H +ATOM 231 H2 TIP3W1014 11.936 15.940 20.591 1.00 0.00 WT1 H +ATOM 232 OH2 TIP3W1017 9.784 18.060 16.439 1.00 0.00 WT1 O +ATOM 233 H1 TIP3W1017 10.576 18.166 15.922 1.00 0.00 WT1 H +ATOM 234 H2 TIP3W1017 9.941 18.584 17.234 1.00 0.00 WT1 H +ATOM 235 OH2 TIP3W1018 2.369 19.620 10.838 1.00 0.00 WT1 O +ATOM 236 H1 TIP3W1018 2.051 19.425 11.701 1.00 0.00 WT1 H +ATOM 237 H2 TIP3W1018 3.347 19.717 10.923 1.00 0.00 WT1 H +ATOM 238 OH2 TIP3W1027 15.158 15.218 1.453 1.00 0.00 WT1 O +ATOM 239 H1 TIP3W1027 15.286 16.123 1.160 1.00 0.00 WT1 H +ATOM 240 H2 TIP3W1027 14.175 15.219 1.587 1.00 0.00 WT1 H +ATOM 241 OH2 TIP3W1032 7.929 9.601 4.322 1.00 0.00 WT1 O +ATOM 242 H1 TIP3W1032 7.364 10.340 3.912 1.00 0.00 WT1 H +ATOM 243 H2 TIP3W1032 7.318 9.011 4.820 1.00 0.00 WT1 H +ATOM 244 OH2 TIP3W1053 11.585 23.121 19.455 1.00 0.00 WT1 O +ATOM 245 H1 TIP3W1053 12.413 23.205 19.982 1.00 0.00 WT1 H +ATOM 246 H2 TIP3W1053 10.816 23.266 20.095 1.00 0.00 WT1 H +ATOM 247 OH2 TIP3W1301 3.320 1.439 3.693 1.00 0.00 WT1 O +ATOM 248 H1 TIP3W1301 3.018 1.263 2.795 1.00 0.00 WT1 H +ATOM 249 H2 TIP3W1301 4.218 1.737 3.533 1.00 0.00 WT1 H +ATOM 250 OH2 TIP3W1308 8.378 22.836 14.074 1.00 0.00 WT1 O +ATOM 251 H1 TIP3W1308 9.127 23.085 13.478 1.00 0.00 WT1 H +ATOM 252 H2 TIP3W1308 7.806 23.652 14.112 1.00 0.00 WT1 H +ATOM 253 OH2 TIP3W1328 4.539 2.605 8.295 1.00 0.00 WT1 O +ATOM 254 H1 TIP3W1328 5.460 2.702 8.123 1.00 0.00 WT1 H +ATOM 255 H2 TIP3W1328 4.434 1.616 8.363 1.00 0.00 WT1 H +ATOM 256 OH2 TIP3W1344 8.883 21.581 5.760 1.00 0.00 WT1 O +ATOM 257 H1 TIP3W1344 8.705 22.232 6.446 1.00 0.00 WT1 H +ATOM 258 H2 TIP3W1344 9.357 22.008 5.077 1.00 0.00 WT1 H +ATOM 259 OH2 TIP3W1349 12.793 13.364 12.168 1.00 0.00 WT1 O +ATOM 260 H1 TIP3W1349 12.787 13.548 11.223 1.00 0.00 WT1 H +ATOM 261 H2 TIP3W1349 11.995 13.794 12.399 1.00 0.00 WT1 H +ATOM 262 OH2 TIP3W1352 6.667 7.547 9.646 1.00 0.00 WT1 O +ATOM 263 H1 TIP3W1352 6.103 6.975 10.296 1.00 0.00 WT1 H +ATOM 264 H2 TIP3W1352 7.558 7.292 10.046 1.00 0.00 WT1 H +ATOM 265 OH2 TIP3W1354 0.182 23.403 21.361 1.00 0.00 WT1 O +ATOM 266 H1 TIP3W1354 0.301 23.585 22.346 1.00 0.00 WT1 H +ATOM 267 H2 TIP3W1354 1.001 22.867 21.220 1.00 0.00 WT1 H +ATOM 268 OH2 TIP3W1355 11.347 16.007 23.148 1.00 0.00 WT1 O +ATOM 269 H1 TIP3W1355 11.779 15.126 23.087 1.00 0.00 WT1 H +ATOM 270 H2 TIP3W1355 10.586 15.923 22.581 1.00 0.00 WT1 H +ATOM 271 OH2 TIP3W1367 10.129 17.485 6.550 1.00 0.00 WT1 O +ATOM 272 H1 TIP3W1367 9.231 17.467 6.920 1.00 0.00 WT1 H +ATOM 273 H2 TIP3W1367 10.108 16.702 5.985 1.00 0.00 WT1 H +ATOM 274 OH2 TIP3W1370 4.654 5.717 5.023 1.00 0.00 WT1 O +ATOM 275 H1 TIP3W1370 5.059 5.126 4.395 1.00 0.00 WT1 H +ATOM 276 H2 TIP3W1370 5.409 5.785 5.634 1.00 0.00 WT1 H +ATOM 277 OH2 TIP3W1371 12.336 14.905 9.350 1.00 0.00 WT1 O +ATOM 278 H1 TIP3W1371 11.849 15.588 8.883 1.00 0.00 WT1 H +ATOM 279 H2 TIP3W1371 11.568 14.375 9.770 1.00 0.00 WT1 H +ATOM 280 OH2 TIP3W1374 5.488 14.255 13.212 1.00 0.00 WT1 O +ATOM 281 H1 TIP3W1374 6.279 14.126 13.709 1.00 0.00 WT1 H +ATOM 282 H2 TIP3W1374 4.864 13.991 13.878 1.00 0.00 WT1 H +ATOM 283 OH2 TIP3W1387 3.686 8.353 3.401 1.00 0.00 WT1 O +ATOM 284 H1 TIP3W1387 4.494 7.930 3.084 1.00 0.00 WT1 H +ATOM 285 H2 TIP3W1387 3.041 7.727 3.197 1.00 0.00 WT1 H +ATOM 286 OH2 TIP3W1388 15.005 14.526 19.133 1.00 0.00 WT1 O +ATOM 287 H1 TIP3W1388 15.742 13.941 19.238 1.00 0.00 WT1 H +ATOM 288 H2 TIP3W1388 14.746 14.453 18.188 1.00 0.00 WT1 H +ATOM 289 OH2 TIP3W1389 15.427 13.899 13.418 1.00 0.00 WT1 O +ATOM 290 H1 TIP3W1389 15.598 14.703 13.915 1.00 0.00 WT1 H +ATOM 291 H2 TIP3W1389 14.569 14.032 12.994 1.00 0.00 WT1 H +ATOM 292 OH2 TIP3W1392 15.117 16.342 15.320 1.00 0.00 WT1 O +ATOM 293 H1 TIP3W1392 14.190 16.658 15.235 1.00 0.00 WT1 H +ATOM 294 H2 TIP3W1392 15.725 17.080 14.950 1.00 0.00 WT1 H +ATOM 295 OH2 TIP3W1407 13.263 23.513 7.326 1.00 0.00 WT1 O +ATOM 296 H1 TIP3W1407 14.083 23.900 7.689 1.00 0.00 WT1 H +ATOM 297 H2 TIP3W1407 13.669 22.803 6.739 1.00 0.00 WT1 H +ATOM 298 OH2 TIP3W1411 10.030 11.441 3.434 1.00 0.00 WT1 O +ATOM 299 H1 TIP3W1411 9.274 10.827 3.422 1.00 0.00 WT1 H +ATOM 300 H2 TIP3W1411 10.533 11.362 2.661 1.00 0.00 WT1 H +ATOM 301 OH2 TIP3W1412 10.550 9.544 11.315 1.00 0.00 WT1 O +ATOM 302 H1 TIP3W1412 10.055 10.343 11.396 1.00 0.00 WT1 H +ATOM 303 H2 TIP3W1412 11.460 9.846 11.337 1.00 0.00 WT1 H +ATOM 304 OH2 TIP3W1414 2.005 17.796 21.122 1.00 0.00 WT1 O +ATOM 305 H1 TIP3W1414 2.773 17.325 21.598 1.00 0.00 WT1 H +ATOM 306 H2 TIP3W1414 2.173 18.758 21.265 1.00 0.00 WT1 H +ATOM 307 OH2 TIP3W1415 13.553 15.240 21.435 1.00 0.00 WT1 O +ATOM 308 H1 TIP3W1415 14.103 14.959 20.726 1.00 0.00 WT1 H +ATOM 309 H2 TIP3W1415 13.422 14.470 21.979 1.00 0.00 WT1 H +ATOM 310 OH2 TIP3W1418 11.456 2.350 19.585 1.00 0.00 WT1 O +ATOM 311 H1 TIP3W1418 10.731 2.931 19.730 1.00 0.00 WT1 H +ATOM 312 H2 TIP3W1418 11.546 1.862 20.401 1.00 0.00 WT1 H +ATOM 313 OH2 TIP3W1428 13.068 2.914 10.149 1.00 0.00 WT1 O +ATOM 314 H1 TIP3W1428 12.803 2.473 9.295 1.00 0.00 WT1 H +ATOM 315 H2 TIP3W1428 14.010 2.849 10.112 1.00 0.00 WT1 H +ATOM 316 OH2 TIP3W1429 5.450 9.067 5.337 1.00 0.00 WT1 O +ATOM 317 H1 TIP3W1429 4.722 8.840 4.711 1.00 0.00 WT1 H +ATOM 318 H2 TIP3W1429 4.939 8.770 6.117 1.00 0.00 WT1 H +ATOM 319 OH2 TIP3W1433 3.297 18.771 17.303 1.00 0.00 WT1 O +ATOM 320 H1 TIP3W1433 3.913 19.272 17.825 1.00 0.00 WT1 H +ATOM 321 H2 TIP3W1433 3.616 18.935 16.408 1.00 0.00 WT1 H +ATOM 322 OH2 TIP3W1435 6.597 15.954 21.463 1.00 0.00 WT1 O +ATOM 323 H1 TIP3W1435 7.157 15.160 21.200 1.00 0.00 WT1 H +ATOM 324 H2 TIP3W1435 7.205 16.451 22.021 1.00 0.00 WT1 H +ATOM 325 OH2 TIP3W1440 1.443 3.980 18.627 1.00 0.00 WT1 O +ATOM 326 H1 TIP3W1440 1.536 3.050 18.247 1.00 0.00 WT1 H +ATOM 327 H2 TIP3W1440 0.589 4.282 18.256 1.00 0.00 WT1 H +ATOM 328 OH2 TIP3W1451 3.248 22.876 3.701 1.00 0.00 WT1 O +ATOM 329 H1 TIP3W1451 2.662 22.334 4.248 1.00 0.00 WT1 H +ATOM 330 H2 TIP3W1451 4.106 22.410 3.781 1.00 0.00 WT1 H +ATOM 331 OH2 TIP3W1454 8.943 19.607 9.393 1.00 0.00 WT1 O +ATOM 332 H1 TIP3W1454 9.890 19.666 9.174 1.00 0.00 WT1 H +ATOM 333 H2 TIP3W1454 8.551 19.202 8.586 1.00 0.00 WT1 H +ATOM 334 OH2 TIP3W1455 7.534 23.313 22.010 1.00 0.00 WT1 O +ATOM 335 H1 TIP3W1455 7.309 22.777 22.738 1.00 0.00 WT1 H +ATOM 336 H2 TIP3W1455 6.697 23.403 21.532 1.00 0.00 WT1 H +ATOM 337 OH2 TIP3W1457 13.340 13.560 16.477 1.00 0.00 WT1 O +ATOM 338 H1 TIP3W1457 13.400 13.568 15.542 1.00 0.00 WT1 H +ATOM 339 H2 TIP3W1457 12.852 14.406 16.633 1.00 0.00 WT1 H +ATOM 340 OH2 TIP3W1458 8.344 7.845 20.429 1.00 0.00 WT1 O +ATOM 341 H1 TIP3W1458 8.479 8.292 21.236 1.00 0.00 WT1 H +ATOM 342 H2 TIP3W1458 9.102 8.059 19.900 1.00 0.00 WT1 H +ATOM 343 OH2 TIP3W1474 6.901 21.557 9.326 1.00 0.00 WT1 O +ATOM 344 H1 TIP3W1474 7.410 20.744 9.384 1.00 0.00 WT1 H +ATOM 345 H2 TIP3W1474 7.474 22.077 8.759 1.00 0.00 WT1 H +ATOM 346 OH2 TIP3W1494 14.403 7.815 15.212 1.00 0.00 WT1 O +ATOM 347 H1 TIP3W1494 13.532 8.206 14.911 1.00 0.00 WT1 H +ATOM 348 H2 TIP3W1494 14.885 7.681 14.373 1.00 0.00 WT1 H +ATOM 349 OH2 TIP3W1497 6.857 11.138 6.829 1.00 0.00 WT1 O +ATOM 350 H1 TIP3W1497 6.107 11.750 6.800 1.00 0.00 WT1 H +ATOM 351 H2 TIP3W1497 6.480 10.387 6.353 1.00 0.00 WT1 H +ATOM 352 OH2 TIP3W1512 10.309 21.500 11.481 1.00 0.00 WT1 O +ATOM 353 H1 TIP3W1512 11.014 20.928 11.185 1.00 0.00 WT1 H +ATOM 354 H2 TIP3W1512 9.595 20.961 11.183 1.00 0.00 WT1 H +ATOM 355 OH2 TIP3W1532 13.235 22.943 15.633 1.00 0.00 WT1 O +ATOM 356 H1 TIP3W1532 12.613 22.525 16.194 1.00 0.00 WT1 H +ATOM 357 H2 TIP3W1532 14.027 22.981 16.180 1.00 0.00 WT1 H +ATOM 358 OH2 TIP3W1559 6.818 20.066 20.150 1.00 0.00 WT1 O +ATOM 359 H1 TIP3W1559 7.686 20.067 20.626 1.00 0.00 WT1 H +ATOM 360 H2 TIP3W1559 6.969 19.869 19.212 1.00 0.00 WT1 H +ATOM 361 OH2 TIP3W1611 7.975 20.030 22.745 1.00 0.00 WT1 O +ATOM 362 H1 TIP3W1611 8.632 20.654 22.435 1.00 0.00 WT1 H +ATOM 363 H2 TIP3W1611 7.441 20.490 23.501 1.00 0.00 WT1 H +ATOM 364 OH2 TIP3W1707 12.113 0.921 4.942 1.00 0.00 WT1 O +ATOM 365 H1 TIP3W1707 12.819 0.635 5.562 1.00 0.00 WT1 H +ATOM 366 H2 TIP3W1707 11.814 1.896 5.223 1.00 0.00 WT1 H +ATOM 367 OH2 TIP3W1723 9.197 4.375 15.964 1.00 0.00 WT1 O +ATOM 368 H1 TIP3W1723 9.163 3.590 15.387 1.00 0.00 WT1 H +ATOM 369 H2 TIP3W1723 8.516 4.167 16.604 1.00 0.00 WT1 H +ATOM 370 OH2 TIP3W1725 2.421 3.775 5.058 1.00 0.00 WT1 O +ATOM 371 H1 TIP3W1725 2.684 2.934 4.652 1.00 0.00 WT1 H +ATOM 372 H2 TIP3W1725 3.219 4.340 5.048 1.00 0.00 WT1 H +ATOM 373 OH2 TIP3W1729 6.794 6.875 22.997 1.00 0.00 WT1 O +ATOM 374 H1 TIP3W1729 7.166 7.815 23.093 1.00 0.00 WT1 H +ATOM 375 H2 TIP3W1729 5.834 7.029 23.036 1.00 0.00 WT1 H +ATOM 376 OH2 TIP3W1730 11.518 2.141 14.835 1.00 0.00 WT1 O +ATOM 377 H1 TIP3W1730 11.356 2.769 14.101 1.00 0.00 WT1 H +ATOM 378 H2 TIP3W1730 12.345 1.727 14.583 1.00 0.00 WT1 H +ATOM 379 OH2 TIP3W1733 3.174 1.584 16.976 1.00 0.00 WT1 O +ATOM 380 H1 TIP3W1733 2.370 2.077 16.810 1.00 0.00 WT1 H +ATOM 381 H2 TIP3W1733 3.270 0.961 16.252 1.00 0.00 WT1 H +ATOM 382 OH2 TIP3W1746 10.848 10.071 18.631 1.00 0.00 WT1 O +ATOM 383 H1 TIP3W1746 10.345 10.477 17.907 1.00 0.00 WT1 H +ATOM 384 H2 TIP3W1746 11.663 10.551 18.638 1.00 0.00 WT1 H +ATOM 385 OH2 TIP3W1752 12.069 8.766 23.082 1.00 0.00 WT1 O +ATOM 386 H1 TIP3W1752 12.023 9.290 23.888 1.00 0.00 WT1 H +ATOM 387 H2 TIP3W1752 11.590 7.956 23.400 1.00 0.00 WT1 H +ATOM 388 OH2 TIP3W1764 5.141 1.611 0.499 1.00 0.00 WT1 O +ATOM 389 H1 TIP3W1764 4.697 1.110 1.234 1.00 0.00 WT1 H +ATOM 390 H2 TIP3W1764 6.031 1.302 0.586 1.00 0.00 WT1 H +ATOM 391 OH2 TIP3W1771 2.509 3.505 12.910 1.00 0.00 WT1 O +ATOM 392 H1 TIP3W1771 2.114 4.138 12.315 1.00 0.00 WT1 H +ATOM 393 H2 TIP3W1771 2.715 2.712 12.383 1.00 0.00 WT1 H +ATOM 394 OH2 TIP3W1773 14.354 1.352 14.004 1.00 0.00 WT1 O +ATOM 395 H1 TIP3W1773 14.694 0.623 14.565 1.00 0.00 WT1 H +ATOM 396 H2 TIP3W1773 14.573 2.195 14.426 1.00 0.00 WT1 H +ATOM 397 OH2 TIP3W1788 14.578 23.489 17.850 1.00 0.00 WT1 O +ATOM 398 H1 TIP3W1788 15.476 23.267 17.861 1.00 0.00 WT1 H +ATOM 399 H2 TIP3W1788 14.359 23.484 18.771 1.00 0.00 WT1 H +ATOM 400 OH2 TIP3W1789 5.461 6.754 1.943 1.00 0.00 WT1 O +ATOM 401 H1 TIP3W1789 6.412 6.627 2.018 1.00 0.00 WT1 H +ATOM 402 H2 TIP3W1789 5.209 5.956 1.434 1.00 0.00 WT1 H +ATOM 403 OH2 TIP3W1795 14.101 1.902 22.316 1.00 0.00 WT1 O +ATOM 404 H1 TIP3W1795 14.886 2.398 22.002 1.00 0.00 WT1 H +ATOM 405 H2 TIP3W1795 14.108 1.041 21.813 1.00 0.00 WT1 H +ATOM 406 OH2 TIP3W1813 6.142 11.858 16.052 1.00 0.00 WT1 O +ATOM 407 H1 TIP3W1813 5.762 12.642 15.675 1.00 0.00 WT1 H +ATOM 408 H2 TIP3W1813 5.566 11.146 15.661 1.00 0.00 WT1 H +ATOM 409 OH2 TIP3W1814 11.187 19.104 18.681 1.00 0.00 WT1 O +ATOM 410 H1 TIP3W1814 12.029 18.566 18.863 1.00 0.00 WT1 H +ATOM 411 H2 TIP3W1814 10.574 18.773 19.364 1.00 0.00 WT1 H +ATOM 412 OH2 TIP3W1829 11.780 13.509 0.983 1.00 0.00 WT1 O +ATOM 413 H1 TIP3W1829 12.311 13.422 1.794 1.00 0.00 WT1 H +ATOM 414 H2 TIP3W1829 12.379 13.816 0.300 1.00 0.00 WT1 H +ATOM 415 OH2 TIP3W1830 13.410 13.796 3.206 1.00 0.00 WT1 O +ATOM 416 H1 TIP3W1830 12.860 13.342 3.952 1.00 0.00 WT1 H +ATOM 417 H2 TIP3W1830 14.378 13.624 3.486 1.00 0.00 WT1 H +ATOM 418 OH2 TIP3W1831 7.314 0.228 9.152 1.00 0.00 WT1 O +ATOM 419 H1 TIP3W1831 7.447 0.196 8.157 1.00 0.00 WT1 H +ATOM 420 H2 TIP3W1831 8.219 0.336 9.426 1.00 0.00 WT1 H +ATOM 421 OH2 TIP3W1853 0.289 10.538 13.468 1.00 0.00 WT1 O +ATOM 422 H1 TIP3W1853 0.286 10.937 12.602 1.00 0.00 WT1 H +ATOM 423 H2 TIP3W1853 1.262 10.357 13.669 1.00 0.00 WT1 H +ATOM 424 OH2 TIP3W1856 12.440 12.407 5.370 1.00 0.00 WT1 O +ATOM 425 H1 TIP3W1856 11.652 11.887 5.105 1.00 0.00 WT1 H +ATOM 426 H2 TIP3W1856 12.893 11.867 5.977 1.00 0.00 WT1 H +ATOM 427 OH2 TIP3W1871 6.968 11.629 2.353 1.00 0.00 WT1 O +ATOM 428 H1 TIP3W1871 6.575 10.896 1.807 1.00 0.00 WT1 H +ATOM 429 H2 TIP3W1871 7.083 12.290 1.590 1.00 0.00 WT1 H +ATOM 430 OH2 TIP3W1873 13.533 10.550 7.160 1.00 0.00 WT1 O +ATOM 431 H1 TIP3W1873 12.608 10.309 7.490 1.00 0.00 WT1 H +ATOM 432 H2 TIP3W1873 14.008 10.940 7.925 1.00 0.00 WT1 H +ATOM 433 OH2 TIP3W1874 13.043 18.831 22.933 1.00 0.00 WT1 O +ATOM 434 H1 TIP3W1874 13.439 17.936 22.986 1.00 0.00 WT1 H +ATOM 435 H2 TIP3W1874 12.139 18.764 23.145 1.00 0.00 WT1 H +ATOM 436 OH2 TIP3W1894 11.706 15.811 16.829 1.00 0.00 WT1 O +ATOM 437 H1 TIP3W1894 10.892 16.347 16.590 1.00 0.00 WT1 H +ATOM 438 H2 TIP3W1894 12.344 16.466 17.162 1.00 0.00 WT1 H +ATOM 439 OH2 TIP3W1911 11.642 19.030 4.866 1.00 0.00 WT1 O +ATOM 440 H1 TIP3W1911 10.752 18.786 5.209 1.00 0.00 WT1 H +ATOM 441 H2 TIP3W1911 11.534 19.147 3.897 1.00 0.00 WT1 H +ATOM 442 OH2 TIP3W1912 13.550 21.522 9.565 1.00 0.00 WT1 O +ATOM 443 H1 TIP3W1912 13.279 21.744 8.655 1.00 0.00 WT1 H +ATOM 444 H2 TIP3W1912 13.859 22.419 9.914 1.00 0.00 WT1 H +ATOM 445 OH2 TIP3W1914 12.001 20.877 14.108 1.00 0.00 WT1 O +ATOM 446 H1 TIP3W1914 12.060 21.566 14.774 1.00 0.00 WT1 H +ATOM 447 H2 TIP3W1914 11.186 21.104 13.629 1.00 0.00 WT1 H +ATOM 448 OH2 TIP3W1915 12.814 17.906 7.383 1.00 0.00 WT1 O +ATOM 449 H1 TIP3W1915 13.379 17.410 6.688 1.00 0.00 WT1 H +ATOM 450 H2 TIP3W1915 11.963 17.994 6.954 1.00 0.00 WT1 H +ATOM 451 OH2 TIP3W1952 15.989 19.751 4.862 1.00 0.00 WT1 O +ATOM 452 H1 TIP3W1952 15.952 20.632 4.460 1.00 0.00 WT1 H +ATOM 453 H2 TIP3W1952 15.557 19.210 4.188 1.00 0.00 WT1 H +ATOM 454 OH2 TIP3W2123 10.963 1.737 11.790 1.00 0.00 WT1 O +ATOM 455 H1 TIP3W2123 10.319 2.240 11.334 1.00 0.00 WT1 H +ATOM 456 H2 TIP3W2123 11.709 2.167 11.210 1.00 0.00 WT1 H +ATOM 457 OH2 TIP3W2163 5.526 8.369 14.858 1.00 0.00 WT1 O +ATOM 458 H1 TIP3W2163 4.950 8.218 14.072 1.00 0.00 WT1 H +ATOM 459 H2 TIP3W2163 4.945 8.919 15.363 1.00 0.00 WT1 H +ATOM 460 OH2 TIP3W2165 14.776 4.939 12.443 1.00 0.00 WT1 O +ATOM 461 H1 TIP3W2165 14.636 5.952 12.252 1.00 0.00 WT1 H +ATOM 462 H2 TIP3W2165 13.865 4.712 12.604 1.00 0.00 WT1 H +ATOM 463 OH2 TIP3W2167 7.529 4.508 1.396 1.00 0.00 WT1 O +ATOM 464 H1 TIP3W2167 8.313 4.582 0.857 1.00 0.00 WT1 H +ATOM 465 H2 TIP3W2167 6.783 4.511 0.768 1.00 0.00 WT1 H +ATOM 466 OH2 TIP3W2172 11.435 0.836 22.059 1.00 0.00 WT1 O +ATOM 467 H1 TIP3W2172 11.858 0.103 21.657 1.00 0.00 WT1 H +ATOM 468 H2 TIP3W2172 12.219 1.281 22.508 1.00 0.00 WT1 H +ATOM 469 OH2 TIP3W2227 11.200 4.151 3.471 1.00 0.00 WT1 O +ATOM 470 H1 TIP3W2227 12.053 4.360 3.928 1.00 0.00 WT1 H +ATOM 471 H2 TIP3W2227 10.572 4.426 4.138 1.00 0.00 WT1 H +ATOM 472 OH2 TIP3W2231 4.884 4.081 13.713 1.00 0.00 WT1 O +ATOM 473 H1 TIP3W2231 4.970 4.746 14.373 1.00 0.00 WT1 H +ATOM 474 H2 TIP3W2231 3.932 3.975 13.593 1.00 0.00 WT1 H +ATOM 475 OH2 TIP3W2244 13.867 4.624 3.954 1.00 0.00 WT1 O +ATOM 476 H1 TIP3W2244 14.067 4.641 4.904 1.00 0.00 WT1 H +ATOM 477 H2 TIP3W2244 14.122 5.494 3.648 1.00 0.00 WT1 H +ATOM 478 OH2 TIP3W2270 3.174 11.159 5.954 1.00 0.00 WT1 O +ATOM 479 H1 TIP3W2270 3.904 11.073 5.352 1.00 0.00 WT1 H +ATOM 480 H2 TIP3W2270 3.204 12.104 6.129 1.00 0.00 WT1 H +ATOM 481 OH2 TIP3W2272 12.922 2.911 17.412 1.00 0.00 WT1 O +ATOM 482 H1 TIP3W2272 12.421 2.431 18.089 1.00 0.00 WT1 H +ATOM 483 H2 TIP3W2272 12.240 2.996 16.701 1.00 0.00 WT1 H +ATOM 484 OH2 TIP3W2277 13.644 7.961 20.946 1.00 0.00 WT1 O +ATOM 485 H1 TIP3W2277 13.183 7.158 20.680 1.00 0.00 WT1 H +ATOM 486 H2 TIP3W2277 13.018 8.315 21.687 1.00 0.00 WT1 H +ATOM 487 OH2 TIP3W2280 6.612 3.396 17.042 1.00 0.00 WT1 O +ATOM 488 H1 TIP3W2280 6.138 2.987 17.830 1.00 0.00 WT1 H +ATOM 489 H2 TIP3W2280 6.248 2.883 16.306 1.00 0.00 WT1 H +ATOM 490 OH2 TIP3W2288 3.628 15.453 9.684 1.00 0.00 WT1 O +ATOM 491 H1 TIP3W2288 3.604 16.368 9.365 1.00 0.00 WT1 H +ATOM 492 H2 TIP3W2288 3.266 15.478 10.592 1.00 0.00 WT1 H +ATOM 493 OH2 TIP3W2293 1.641 18.264 8.136 1.00 0.00 WT1 O +ATOM 494 H1 TIP3W2293 0.755 18.490 8.008 1.00 0.00 WT1 H +ATOM 495 H2 TIP3W2293 1.981 19.003 8.665 1.00 0.00 WT1 H +ATOM 496 OH2 TIP3W2295 8.716 0.819 21.571 1.00 0.00 WT1 O +ATOM 497 H1 TIP3W2295 8.359 0.399 22.460 1.00 0.00 WT1 H +ATOM 498 H2 TIP3W2295 9.622 1.046 21.690 1.00 0.00 WT1 H +ATOM 499 OH2 TIP3W2309 14.269 10.001 4.369 1.00 0.00 WT1 O +ATOM 500 H1 TIP3W2309 14.973 10.528 4.752 1.00 0.00 WT1 H +ATOM 501 H2 TIP3W2309 13.690 9.859 5.092 1.00 0.00 WT1 H +ATOM 502 OH2 TIP3W2311 14.691 13.817 9.050 1.00 0.00 WT1 O +ATOM 503 H1 TIP3W2311 15.162 14.372 8.385 1.00 0.00 WT1 H +ATOM 504 H2 TIP3W2311 13.821 14.250 9.113 1.00 0.00 WT1 H +ATOM 505 OH2 TIP3W2316 12.273 5.424 10.404 1.00 0.00 WT1 O +ATOM 506 H1 TIP3W2316 12.384 4.472 10.210 1.00 0.00 WT1 H +ATOM 507 H2 TIP3W2316 13.153 5.714 10.501 1.00 0.00 WT1 H +ATOM 508 OH2 TIP3W2317 3.759 13.253 15.143 1.00 0.00 WT1 O +ATOM 509 H1 TIP3W2317 3.552 13.546 16.059 1.00 0.00 WT1 H +ATOM 510 H2 TIP3W2317 2.862 13.321 14.740 1.00 0.00 WT1 H +ATOM 511 OH2 TIP3W2335 7.319 14.432 15.015 1.00 0.00 WT1 O +ATOM 512 H1 TIP3W2335 7.633 15.319 14.742 1.00 0.00 WT1 H +ATOM 513 H2 TIP3W2335 7.702 14.303 15.933 1.00 0.00 WT1 H +ATOM 514 OH2 TIP3W2357 3.117 11.819 10.070 1.00 0.00 WT1 O +ATOM 515 H1 TIP3W2357 3.490 12.496 9.523 1.00 0.00 WT1 H +ATOM 516 H2 TIP3W2357 3.937 11.583 10.539 1.00 0.00 WT1 H +ATOM 517 OH2 TIP3W2358 0.549 16.393 10.366 1.00 0.00 WT1 O +ATOM 518 H1 TIP3W2358 1.292 16.322 11.016 1.00 0.00 WT1 H +ATOM 519 H2 TIP3W2358 0.665 17.283 9.972 1.00 0.00 WT1 H +ATOM 520 OH2 TIP3W2607 10.050 5.605 5.758 1.00 0.00 WT1 O +ATOM 521 H1 TIP3W2607 10.155 6.554 5.556 1.00 0.00 WT1 H +ATOM 522 H2 TIP3W2607 10.797 5.389 6.309 1.00 0.00 WT1 H +ATOM 523 OH2 TIP3W2608 7.881 3.518 5.700 1.00 0.00 WT1 O +ATOM 524 H1 TIP3W2608 8.550 4.225 5.812 1.00 0.00 WT1 H +ATOM 525 H2 TIP3W2608 7.070 3.834 6.169 1.00 0.00 WT1 H +ATOM 526 OH2 TIP3W2634 8.559 3.515 11.535 1.00 0.00 WT1 O +ATOM 527 H1 TIP3W2634 8.435 4.298 12.155 1.00 0.00 WT1 H +ATOM 528 H2 TIP3W2634 7.955 2.899 11.952 1.00 0.00 WT1 H +ATOM 529 OH2 TIP3W2669 13.039 10.511 11.777 1.00 0.00 WT1 O +ATOM 530 H1 TIP3W2669 13.825 10.589 11.282 1.00 0.00 WT1 H +ATOM 531 H2 TIP3W2669 12.883 11.473 11.916 1.00 0.00 WT1 H +ATOM 532 OH2 TIP3W2691 15.316 3.976 15.033 1.00 0.00 WT1 O +ATOM 533 H1 TIP3W2691 15.353 4.265 14.065 1.00 0.00 WT1 H +ATOM 534 H2 TIP3W2691 14.585 4.533 15.460 1.00 0.00 WT1 H +ATOM 535 OH2 TIP3W2694 8.400 5.552 13.557 1.00 0.00 WT1 O +ATOM 536 H1 TIP3W2694 9.070 5.240 14.185 1.00 0.00 WT1 H +ATOM 537 H2 TIP3W2694 7.739 5.945 14.163 1.00 0.00 WT1 H +ATOM 538 OH2 TIP3W2714 4.281 21.161 19.066 1.00 0.00 WT1 O +ATOM 539 H1 TIP3W2714 5.157 21.058 19.381 1.00 0.00 WT1 H +ATOM 540 H2 TIP3W2714 4.169 22.110 18.904 1.00 0.00 WT1 H +ATOM 541 OH2 TIP3W2732 13.870 7.474 12.187 1.00 0.00 WT1 O +ATOM 542 H1 TIP3W2732 13.209 8.073 12.633 1.00 0.00 WT1 H +ATOM 543 H2 TIP3W2732 14.457 8.029 11.659 1.00 0.00 WT1 H +ATOM 544 OH2 TIP3W2735 13.600 17.247 9.998 1.00 0.00 WT1 O +ATOM 545 H1 TIP3W2735 13.256 16.385 10.107 1.00 0.00 WT1 H +ATOM 546 H2 TIP3W2735 13.616 17.337 9.047 1.00 0.00 WT1 H +ATOM 547 OH2 TIP3W2758 10.099 18.083 21.099 1.00 0.00 WT1 O +ATOM 548 H1 TIP3W2758 10.453 17.258 20.699 1.00 0.00 WT1 H +ATOM 549 H2 TIP3W2758 9.398 17.746 21.690 1.00 0.00 WT1 H +ATOM 550 OH2 TIP3W2778 15.465 7.955 17.814 1.00 0.00 WT1 O +ATOM 551 H1 TIP3W2778 15.150 7.979 16.932 1.00 0.00 WT1 H +ATOM 552 H2 TIP3W2778 14.706 7.563 18.306 1.00 0.00 WT1 H +ATOM 553 OH2 TIP3W3010 9.016 4.086 8.814 1.00 0.00 WT1 O +ATOM 554 H1 TIP3W3010 9.377 5.001 8.813 1.00 0.00 WT1 H +ATOM 555 H2 TIP3W3010 8.726 3.741 9.661 1.00 0.00 WT1 H +ATOM 556 OH2 TIP3W3072 6.439 5.144 7.455 1.00 0.00 WT1 O +ATOM 557 H1 TIP3W3072 7.310 4.836 7.837 1.00 0.00 WT1 H +ATOM 558 H2 TIP3W3072 6.121 5.819 8.116 1.00 0.00 WT1 H +ATOM 559 OH2 TIP3W3096 13.331 4.563 23.416 1.00 0.00 WT1 O +ATOM 560 H1 TIP3W3096 14.315 4.772 23.360 1.00 0.00 WT1 H +ATOM 561 H2 TIP3W3096 13.215 3.678 23.134 1.00 0.00 WT1 H +ATOM 562 OH2 TIP3W3134 11.401 21.480 17.136 1.00 0.00 WT1 O +ATOM 563 H1 TIP3W3134 11.522 22.112 17.856 1.00 0.00 WT1 H +ATOM 564 H2 TIP3W3134 11.255 20.672 17.636 1.00 0.00 WT1 H +ATOM 565 OH2 TIP3W3173 12.076 4.645 13.566 1.00 0.00 WT1 O +ATOM 566 H1 TIP3W3173 12.000 5.522 13.148 1.00 0.00 WT1 H +ATOM 567 H2 TIP3W3173 11.827 4.835 14.443 1.00 0.00 WT1 H +ATOM 568 OH2 TIP3W3177 9.131 1.075 15.841 1.00 0.00 WT1 O +ATOM 569 H1 TIP3W3177 9.948 1.463 15.412 1.00 0.00 WT1 H +ATOM 570 H2 TIP3W3177 9.113 0.161 15.464 1.00 0.00 WT1 H +ATOM 571 OH2 TIP3W3196 7.694 8.338 16.687 1.00 0.00 WT1 O +ATOM 572 H1 TIP3W3196 7.323 8.081 17.508 1.00 0.00 WT1 H +ATOM 573 H2 TIP3W3196 6.991 8.476 16.072 1.00 0.00 WT1 H +ATOM 574 OH2 TIP3W3218 11.912 13.212 19.726 1.00 0.00 WT1 O +ATOM 575 H1 TIP3W3218 12.854 13.225 19.881 1.00 0.00 WT1 H +ATOM 576 H2 TIP3W3218 11.504 12.764 20.555 1.00 0.00 WT1 H +ATOM 577 OH2 TIP3W3223 5.115 19.820 22.632 1.00 0.00 WT1 O +ATOM 578 H1 TIP3W3223 4.270 19.752 22.092 1.00 0.00 WT1 H +ATOM 579 H2 TIP3W3223 5.800 19.585 21.996 1.00 0.00 WT1 H +ATOM 580 OH2 TIP3W3303 14.170 23.047 20.478 1.00 0.00 WT1 O +ATOM 581 H1 TIP3W3303 15.015 22.883 20.902 1.00 0.00 WT1 H +ATOM 582 H2 TIP3W3303 13.757 22.177 20.579 1.00 0.00 WT1 H +ATOM 583 OH2 TIP3W3304 13.163 20.489 20.636 1.00 0.00 WT1 O +ATOM 584 H1 TIP3W3304 12.450 20.171 20.104 1.00 0.00 WT1 H +ATOM 585 H2 TIP3W3304 13.220 19.875 21.393 1.00 0.00 WT1 H +ATOM 586 OH2 TIP3W3447 11.316 2.273 7.956 1.00 0.00 WT1 O +ATOM 587 H1 TIP3W3447 11.391 1.358 8.151 1.00 0.00 WT1 H +ATOM 588 H2 TIP3W3447 10.423 2.479 8.181 1.00 0.00 WT1 H +ATOM 589 OH2 TIP3W3545 10.407 6.649 8.888 1.00 0.00 WT1 O +ATOM 590 H1 TIP3W3545 9.810 7.215 9.386 1.00 0.00 WT1 H +ATOM 591 H2 TIP3W3545 11.077 6.417 9.547 1.00 0.00 WT1 H +ATOM 592 OH2 TIP3W3596 7.574 19.420 4.717 1.00 0.00 WT1 O +ATOM 593 H1 TIP3W3596 7.704 19.335 3.679 1.00 0.00 WT1 H +ATOM 594 H2 TIP3W3596 7.970 20.255 4.957 1.00 0.00 WT1 H +ATOM 595 OH2 TIP3W3650 12.254 19.676 2.229 1.00 0.00 WT1 O +ATOM 596 H1 TIP3W3650 12.678 20.538 2.358 1.00 0.00 WT1 H +ATOM 597 H2 TIP3W3650 12.115 19.535 1.250 1.00 0.00 WT1 H +ATOM 598 OH2 TIP3W3660 14.036 7.730 6.644 1.00 0.00 WT1 O +ATOM 599 H1 TIP3W3660 14.358 7.138 7.346 1.00 0.00 WT1 H +ATOM 600 H2 TIP3W3660 13.886 8.589 7.123 1.00 0.00 WT1 H +ATOM 601 OH2 TIP3W3977 8.900 7.310 11.290 1.00 0.00 WT1 O +ATOM 602 H1 TIP3W3977 8.739 6.706 12.078 1.00 0.00 WT1 H +ATOM 603 H2 TIP3W3977 9.555 8.003 11.531 1.00 0.00 WT1 H +ATOM 604 OH2 TIP3W4012 9.495 14.416 1.979 1.00 0.00 WT1 O +ATOM 605 H1 TIP3W4012 10.354 14.203 1.548 1.00 0.00 WT1 H +ATOM 606 H2 TIP3W4012 9.165 13.566 2.099 1.00 0.00 WT1 H +ATOM 607 OH2 TIP3W4036 13.605 5.353 19.280 1.00 0.00 WT1 O +ATOM 608 H1 TIP3W4036 13.658 4.527 18.812 1.00 0.00 WT1 H +ATOM 609 H2 TIP3W4036 12.688 5.367 19.516 1.00 0.00 WT1 H +ATOM 610 OH2 TIP3W4074 7.334 17.973 7.090 1.00 0.00 WT1 O +ATOM 611 H1 TIP3W4074 7.571 18.390 6.200 1.00 0.00 WT1 H +ATOM 612 H2 TIP3W4074 6.533 17.444 6.885 1.00 0.00 WT1 H +ATOM 613 OH2 TIP3W4077 13.912 11.040 17.383 1.00 0.00 WT1 O +ATOM 614 H1 TIP3W4077 13.913 10.932 16.423 1.00 0.00 WT1 H +ATOM 615 H2 TIP3W4077 13.612 11.935 17.518 1.00 0.00 WT1 H +ATOM 616 OH2 TIP3W4501 14.682 11.334 14.388 1.00 0.00 WT1 O +ATOM 617 H1 TIP3W4501 15.236 11.941 13.876 1.00 0.00 WT1 H +ATOM 618 H2 TIP3W4501 14.266 10.683 13.763 1.00 0.00 WT1 H +ATOM 619 OH2 TIP3W4515 12.414 9.004 13.909 1.00 0.00 WT1 O +ATOM 620 H1 TIP3W4515 11.523 8.931 14.184 1.00 0.00 WT1 H +ATOM 621 H2 TIP3W4515 12.375 9.766 13.286 1.00 0.00 WT1 H +ATOM 622 OH2 TIP3W4809 15.898 3.293 1.648 1.00 0.00 WT1 O +ATOM 623 H1 TIP3W4809 15.837 3.977 2.359 1.00 0.00 WT1 H +ATOM 624 H2 TIP3W4809 15.065 2.796 1.789 1.00 0.00 WT1 H +ATOM 625 OH2 TIP3W6240 3.080 0.949 11.788 1.00 0.00 WT1 O +ATOM 626 H1 TIP3W6240 3.690 0.500 11.172 1.00 0.00 WT1 H +ATOM 627 H2 TIP3W6240 2.196 0.556 11.641 1.00 0.00 WT1 H +ATOM 628 OH2 TIP3W6671 0.897 12.813 20.940 1.00 0.00 WT1 O +ATOM 629 H1 TIP3W6671 1.234 13.577 21.489 1.00 0.00 WT1 H +ATOM 630 H2 TIP3W6671 1.110 12.083 21.442 1.00 0.00 WT1 H +ATOM 631 OH2 TIP3W7222 6.255 9.802 0.364 1.00 0.00 WT1 O +ATOM 632 H1 TIP3W7222 6.954 9.121 0.671 1.00 0.00 WT1 H +ATOM 633 H2 TIP3W7222 5.459 9.264 0.196 1.00 0.00 WT1 H +ATOM 634 OH2 TIP3W7479 6.140 3.669 3.704 1.00 0.00 WT1 O +ATOM 635 H1 TIP3W7479 6.732 3.837 2.949 1.00 0.00 WT1 H +ATOM 636 H2 TIP3W7479 6.807 3.408 4.378 1.00 0.00 WT1 H +ATOM 637 OH2 TIP3W7510 5.150 11.685 11.994 1.00 0.00 WT1 O +ATOM 638 H1 TIP3W7510 5.312 12.641 12.020 1.00 0.00 WT1 H +ATOM 639 H2 TIP3W7510 5.614 11.405 12.778 1.00 0.00 WT1 H +ATOM 640 OH2 TIP3W7563 5.196 19.304 15.315 1.00 0.00 WT1 O +ATOM 641 H1 TIP3W7563 5.227 20.213 14.942 1.00 0.00 WT1 H +ATOM 642 H2 TIP3W7563 5.252 18.720 14.569 1.00 0.00 WT1 H +ATOM 643 OH2 TIP3W7630 2.179 13.464 7.177 1.00 0.00 WT1 O +ATOM 644 H1 TIP3W7630 2.719 14.061 7.737 1.00 0.00 WT1 H +ATOM 645 H2 TIP3W7630 1.640 13.021 7.843 1.00 0.00 WT1 H +ATOM 646 OH2 TIP3W7631 1.926 21.439 17.027 1.00 0.00 WT1 O +ATOM 647 H1 TIP3W7631 2.672 21.817 16.545 1.00 0.00 WT1 H +ATOM 648 H2 TIP3W7631 2.398 20.912 17.662 1.00 0.00 WT1 H +ATOM 649 OH2 TIP3W7707 0.688 2.781 7.114 1.00 0.00 WT1 O +ATOM 650 H1 TIP3W7707 1.488 3.190 6.703 1.00 0.00 WT1 H +ATOM 651 H2 TIP3W7707 0.053 3.429 6.930 1.00 0.00 WT1 H +ATOM 652 OH2 TIP3W7985 0.449 7.366 9.140 1.00 0.00 WT1 O +ATOM 653 H1 TIP3W7985 0.202 6.479 9.095 1.00 0.00 WT1 H +ATOM 654 H2 TIP3W7985 0.796 7.563 8.256 1.00 0.00 WT1 H +ATOM 655 OH2 TIP3W8023 0.913 12.320 0.937 1.00 0.00 WT1 O +ATOM 656 H1 TIP3W8023 0.623 11.700 0.268 1.00 0.00 WT1 H +ATOM 657 H2 TIP3W8023 1.290 11.784 1.628 1.00 0.00 WT1 H +ATOM 658 OH2 TIP3W8029 7.889 16.997 14.360 1.00 0.00 WT1 O +ATOM 659 H1 TIP3W8029 7.935 17.181 13.358 1.00 0.00 WT1 H +ATOM 660 H2 TIP3W8029 8.602 17.562 14.734 1.00 0.00 WT1 H +ATOM 661 OH2 TIP3W8046 3.230 22.882 11.736 1.00 0.00 WT1 O +ATOM 662 H1 TIP3W8046 3.601 21.950 11.670 1.00 0.00 WT1 H +ATOM 663 H2 TIP3W8046 2.861 22.992 10.853 1.00 0.00 WT1 H +ATOM 664 OH2 TIP3W8064 4.620 22.335 7.130 1.00 0.00 WT1 O +ATOM 665 H1 TIP3W8064 3.754 22.591 7.590 1.00 0.00 WT1 H +ATOM 666 H2 TIP3W8064 5.178 22.349 7.907 1.00 0.00 WT1 H +ATOM 667 OH2 TIP3W8068 1.124 22.962 13.514 1.00 0.00 WT1 O +ATOM 668 H1 TIP3W8068 1.837 22.901 12.860 1.00 0.00 WT1 H +ATOM 669 H2 TIP3W8068 0.685 23.799 13.310 1.00 0.00 WT1 H +ATOM 670 OH2 TIP3W8364 8.561 10.924 16.881 1.00 0.00 WT1 O +ATOM 671 H1 TIP3W8364 7.916 11.188 16.202 1.00 0.00 WT1 H +ATOM 672 H2 TIP3W8364 8.309 10.008 17.123 1.00 0.00 WT1 H +ATOM 673 OH2 TIP3W8403 4.751 19.009 2.814 1.00 0.00 WT1 O +ATOM 674 H1 TIP3W8403 4.754 18.978 3.760 1.00 0.00 WT1 H +ATOM 675 H2 TIP3W8403 5.300 18.306 2.612 1.00 0.00 WT1 H +ATOM 676 OH2 TIP3W8411 3.406 0.117 14.493 1.00 0.00 WT1 O +ATOM 677 H1 TIP3W8411 3.348 0.244 13.546 1.00 0.00 WT1 H +ATOM 678 H2 TIP3W8411 4.378 0.190 14.724 1.00 0.00 WT1 H +ATOM 679 OH2 TIP3W8425 2.278 3.922 1.200 1.00 0.00 WT1 O +ATOM 680 H1 TIP3W8425 2.701 3.392 0.560 1.00 0.00 WT1 H +ATOM 681 H2 TIP3W8425 1.556 3.406 1.415 1.00 0.00 WT1 H +ATOM 682 OH2 TIP3W8441 6.246 21.216 13.564 1.00 0.00 WT1 O +ATOM 683 H1 TIP3W8441 7.127 21.533 13.794 1.00 0.00 WT1 H +ATOM 684 H2 TIP3W8441 5.802 22.075 13.455 1.00 0.00 WT1 H +ATOM 685 OH2 TIP3W8466 5.348 15.459 5.988 1.00 0.00 WT1 O +ATOM 686 H1 TIP3W8466 4.942 16.211 6.465 1.00 0.00 WT1 H +ATOM 687 H2 TIP3W8466 4.964 14.679 6.422 1.00 0.00 WT1 H +ATOM 688 OH2 TIP3W8468 1.312 13.577 13.829 1.00 0.00 WT1 O +ATOM 689 H1 TIP3W8468 1.594 13.350 12.963 1.00 0.00 WT1 H +ATOM 690 H2 TIP3W8468 0.905 14.443 13.634 1.00 0.00 WT1 H +ATOM 691 OH2 TIP3W8491 10.395 21.375 22.397 1.00 0.00 WT1 O +ATOM 692 H1 TIP3W8491 10.900 20.680 22.794 1.00 0.00 WT1 H +ATOM 693 H2 TIP3W8491 10.682 22.154 22.828 1.00 0.00 WT1 H +ATOM 694 OH2 TIP3W8528 6.013 16.085 3.326 1.00 0.00 WT1 O +ATOM 695 H1 TIP3W8528 6.016 16.035 4.292 1.00 0.00 WT1 H +ATOM 696 H2 TIP3W8528 5.249 15.516 3.046 1.00 0.00 WT1 H +ATOM 697 OH2 TIP3W8534 2.184 22.110 9.500 1.00 0.00 WT1 O +ATOM 698 H1 TIP3W8534 1.913 21.297 9.998 1.00 0.00 WT1 H +ATOM 699 H2 TIP3W8534 1.389 22.233 8.964 1.00 0.00 WT1 H +ATOM 700 OH2 TIP3W8536 3.207 13.979 17.772 1.00 0.00 WT1 O +ATOM 701 H1 TIP3W8536 3.947 14.082 18.373 1.00 0.00 WT1 H +ATOM 702 H2 TIP3W8536 2.585 14.685 17.921 1.00 0.00 WT1 H +ATOM 703 OH2 TIP3W8548 13.639 16.098 5.269 1.00 0.00 WT1 O +ATOM 704 H1 TIP3W8548 14.099 15.394 4.872 1.00 0.00 WT1 H +ATOM 705 H2 TIP3W8548 12.755 15.724 5.343 1.00 0.00 WT1 H +ATOM 706 OH2 TIP3W8556 1.981 16.635 18.663 1.00 0.00 WT1 O +ATOM 707 H1 TIP3W8556 1.921 17.181 19.529 1.00 0.00 WT1 H +ATOM 708 H2 TIP3W8556 2.656 17.117 18.156 1.00 0.00 WT1 H +ATOM 709 OH2 TIP3W8760 13.457 20.491 6.545 1.00 0.00 WT1 O +ATOM 710 H1 TIP3W8760 13.544 19.713 6.959 1.00 0.00 WT1 H +ATOM 711 H2 TIP3W8760 13.199 20.170 5.601 1.00 0.00 WT1 H +ATOM 712 OH2 TIP3W8780 3.438 8.099 0.316 1.00 0.00 WT1 O +ATOM 713 H1 TIP3W8780 2.547 7.847 0.577 1.00 0.00 WT1 H +ATOM 714 H2 TIP3W8780 3.889 7.775 1.093 1.00 0.00 WT1 H +ATOM 715 OH2 TIP3W8801 9.016 15.690 9.485 1.00 0.00 WT1 O +ATOM 716 H1 TIP3W8801 9.158 14.769 9.701 1.00 0.00 WT1 H +ATOM 717 H2 TIP3W8801 8.537 15.554 8.652 1.00 0.00 WT1 H +ATOM 718 OH2 TIP3W8822 1.562 6.536 12.239 1.00 0.00 WT1 O +ATOM 719 H1 TIP3W8822 0.960 7.250 12.049 1.00 0.00 WT1 H +ATOM 720 H2 TIP3W8822 1.197 5.827 11.553 1.00 0.00 WT1 H +ATOM 721 OH2 TIP3W8829 1.314 9.385 7.173 1.00 0.00 WT1 O +ATOM 722 H1 TIP3W8829 1.333 8.706 6.444 1.00 0.00 WT1 H +ATOM 723 H2 TIP3W8829 2.056 9.953 6.980 1.00 0.00 WT1 H +ATOM 724 OH2 TIP3W8843 7.572 0.420 3.478 1.00 0.00 WT1 O +ATOM 725 H1 TIP3W8843 7.636 0.339 2.503 1.00 0.00 WT1 H +ATOM 726 H2 TIP3W8843 6.628 0.234 3.530 1.00 0.00 WT1 H +ATOM 727 OH2 TIP3W8845 1.133 7.080 5.078 1.00 0.00 WT1 O +ATOM 728 H1 TIP3W8845 1.201 7.102 4.137 1.00 0.00 WT1 H +ATOM 729 H2 TIP3W8845 0.358 6.549 5.302 1.00 0.00 WT1 H +ATOM 730 OH2 TIP3W8865 11.515 22.342 4.827 1.00 0.00 WT1 O +ATOM 731 H1 TIP3W8865 10.875 21.911 4.185 1.00 0.00 WT1 H +ATOM 732 H2 TIP3W8865 11.205 21.919 5.694 1.00 0.00 WT1 H +ATOM 733 OH2 TIP3W8869 5.279 5.755 11.457 1.00 0.00 WT1 O +ATOM 734 H1 TIP3W8869 4.504 5.333 10.967 1.00 0.00 WT1 H +ATOM 735 H2 TIP3W8869 5.564 4.986 12.019 1.00 0.00 WT1 H +ATOM 736 OH2 TIP3W8887 8.890 21.041 16.070 1.00 0.00 WT1 O +ATOM 737 H1 TIP3W8887 8.698 21.572 15.300 1.00 0.00 WT1 H +ATOM 738 H2 TIP3W8887 9.800 21.340 16.244 1.00 0.00 WT1 H +ATOM 739 OH2 TIP3W8895 6.000 11.283 22.324 1.00 0.00 WT1 O +ATOM 740 H1 TIP3W8895 5.866 12.057 22.939 1.00 0.00 WT1 H +ATOM 741 H2 TIP3W8895 5.863 11.634 21.452 1.00 0.00 WT1 H +ATOM 742 OH2 TIP3W8905 7.834 14.408 7.527 1.00 0.00 WT1 O +ATOM 743 H1 TIP3W8905 7.105 14.717 6.993 1.00 0.00 WT1 H +ATOM 744 H2 TIP3W8905 8.194 13.714 6.926 1.00 0.00 WT1 H +ATOM 745 OH2 TIP3W8931 5.667 11.812 19.542 1.00 0.00 WT1 O +ATOM 746 H1 TIP3W8931 5.647 12.743 19.497 1.00 0.00 WT1 H +ATOM 747 H2 TIP3W8931 5.889 11.629 18.618 1.00 0.00 WT1 H +ATOM 748 OH2 TIP3W8932 12.997 18.576 15.207 1.00 0.00 WT1 O +ATOM 749 H1 TIP3W8932 12.617 19.193 14.493 1.00 0.00 WT1 H +ATOM 750 H2 TIP3W8932 13.582 19.163 15.737 1.00 0.00 WT1 H +ATOM 751 OH2 TIP3W8935 0.675 11.574 10.952 1.00 0.00 WT1 O +ATOM 752 H1 TIP3W8935 1.597 11.546 10.574 1.00 0.00 WT1 H +ATOM 753 H2 TIP3W8935 0.265 12.150 10.339 1.00 0.00 WT1 H +ATOM 754 OH2 TIP3W8949 8.782 17.187 2.362 1.00 0.00 WT1 O +ATOM 755 H1 TIP3W8949 8.004 16.786 2.797 1.00 0.00 WT1 H +ATOM 756 H2 TIP3W8949 9.140 16.422 1.970 1.00 0.00 WT1 H +ATOM 757 OH2 TIP3W8956 2.113 6.516 21.893 1.00 0.00 WT1 O +ATOM 758 H1 TIP3W8956 2.170 5.576 22.160 1.00 0.00 WT1 H +ATOM 759 H2 TIP3W8956 2.446 6.949 22.707 1.00 0.00 WT1 H +ATOM 760 OH2 TIP3W8977 2.583 16.123 12.046 1.00 0.00 WT1 O +ATOM 761 H1 TIP3W8977 3.491 16.508 12.059 1.00 0.00 WT1 H +ATOM 762 H2 TIP3W8977 2.312 16.312 12.887 1.00 0.00 WT1 H +ATOM 763 OH2 TIP3W8988 2.246 20.883 4.995 1.00 0.00 WT1 O +ATOM 764 H1 TIP3W8988 1.611 20.097 4.885 1.00 0.00 WT1 H +ATOM 765 H2 TIP3W8988 3.079 20.473 5.195 1.00 0.00 WT1 H +ATOM 766 OH2 TIP3W9082 8.156 17.564 11.520 1.00 0.00 WT1 O +ATOM 767 H1 TIP3W9082 8.355 18.345 10.921 1.00 0.00 WT1 H +ATOM 768 H2 TIP3W9082 8.334 16.820 10.874 1.00 0.00 WT1 H +ATOM 769 OH2 TIP3W9096 2.915 14.197 3.393 1.00 0.00 WT1 O +ATOM 770 H1 TIP3W9096 2.155 14.414 3.916 1.00 0.00 WT1 H +ATOM 771 H2 TIP3W9096 2.719 13.333 3.011 1.00 0.00 WT1 H +ATOM 772 OH2 TIP3W9226 8.578 0.832 6.351 1.00 0.00 WT1 O +ATOM 773 H1 TIP3W9226 7.928 0.530 5.693 1.00 0.00 WT1 H +ATOM 774 H2 TIP3W9226 8.563 1.801 6.335 1.00 0.00 WT1 H +ATOM 775 OH2 TIP3W9241 7.287 10.172 13.815 1.00 0.00 WT1 O +ATOM 776 H1 TIP3W9241 6.631 9.473 14.077 1.00 0.00 WT1 H +ATOM 777 H2 TIP3W9241 8.119 9.669 13.852 1.00 0.00 WT1 H +ATOM 778 OH2 TIP3W9250 3.347 10.487 19.814 1.00 0.00 WT1 O +ATOM 779 H1 TIP3W9250 2.792 10.955 19.188 1.00 0.00 WT1 H +ATOM 780 H2 TIP3W9250 4.264 10.639 19.456 1.00 0.00 WT1 H +END diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt new file mode 100644 index 000000000..019911c19 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt @@ -0,0 +1,52 @@ +# file "spce.lt" +# +# H1 H2 +# \ / +# O + +SPCE { + + write_once("In Init") { + # -- Default styles (for solo "SPCE" water) -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 + $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 + } + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 1000.0 1.0 + angle_coeff @angle:HOH harmonic 1000.0 109.47 + pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + group spce type @atom:O @atom:H + fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fShakeSPCE during minimization.) + } + +} # end of definition of "SPCE" water molecule type + diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt new file mode 100644 index 000000000..274d8aeb1 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt @@ -0,0 +1,16 @@ +import "spce.lt" + +wat = new SPCE [260] + + + + + + + +# Open up the PDB file to count the number of water molecules inside. (Or just +# divide the number of atoms by 3). Put that in between the brackets ("[260]") +# +# The command above does not set the positions of the atoms. +# So they will have to be loaded later from a PDB or an XYZ file. +# (For example, using "moltemplate.sh -pdb solvate.pdb system.lt") diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt new file mode 100644 index 000000000..4d8af42b5 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt @@ -0,0 +1,48 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- + +# Note: The minimization step is not necessary in this example. However +# in general, it's always a good idea to minimize the system beforehand. +# fShakeSPCE was defined in system.in.settings. It is incompatible with "minimize". +unfix fShakeSPCE +minimize 1.0e-3 1.0e-5 100000 400000 +# Now read "system.in.settings" in order to redefine fShakeSPCE again: +include system.in.settings + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 +thermo 100 + +run 10000 + +# Now that the system's temperature has become more equilibrated, +# we can increase the timestep: + +timestep 2.0 +run 50000 + +write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt new file mode 100644 index 000000000..22fb1f271 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt @@ -0,0 +1,58 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_npt.data + + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- +# Note: If you are reading the restart file instead of the data file, +# then you should not need to minimize the system beforehand.. +# fShakeSPCE was defined in system.in.settings. +# (It is incompatible with "minimize".) +unfix fShakeSPCE +minimize 1.0e-5 1.0e-7 100000 400000 +# Now read "system.in.settings" in order to redefine fShakeSPCE again: +include system.in.settings + +# -- simulation protocol -- + + + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 +thermo 500 + +run 10000 + +# Now that the system's temperature has become more equilibrated, +# we can increase the timestep: + +timestep 2.0 +run 50000 + +write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_run.sh b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_run.sh new file mode 100755 index 000000000..cf51fa870 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_run.sh @@ -0,0 +1,33 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure + +# or + +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation are ignored when beginning the simulation at constant volume. +# This can be fixed. Read "run.in.nvt" for equilibration instructions.) + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +# or +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_setup.sh new file mode 100755 index 000000000..3a0821269 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -atomstyle full system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_visualize.txt new file mode 100644 index 000000000..019afc144 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Cl.jpg b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Cl.jpg new file mode 100644 index 000000000..5261bedc2 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Cl.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Na.jpg b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Na.jpg new file mode 100644 index 000000000..78c4056f8 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Na.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 000000000..d255bf368 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,4257 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 3016 !NATOM + 1 1 3 3 -0.847600 15.9994 0 + 2 1 4 4 0.423800 1.0080 0 + 3 1 4 4 0.423800 1.0080 0 + 4 2 3 3 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a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg new file mode 100644 index 000000000..220a71727 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/ions.lt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/ions.lt new file mode 100644 index 000000000..0e080db74 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/ions.lt @@ -0,0 +1,60 @@ +# We define two molecule classes to represent Na+ and Cl- ions, respectively. +# This may seem like overkill since they both only consist of one atom each. + + +# Note: Monovalent ion parameters for Ewald and SPC/E water +# are from: Joung & Cheatham JPCB (2008) +# These Lennard Jones parameters match the parameters for ions +# in SPC/E water in the "frcmod.ionsjc_spce" file distributed +# with Amber (the 2010 version). + + +NaIon { + write_once("In Settings") { + pair_coeff @atom:Na @atom:Na lj/charmm/coul/long 0.3526418 1.212 + } + + write_once("Data Masses") { + @atom:Na 22.9898 + } + + # assumes "full" atom style + write("Data Atoms") { + $atom:Na $mol @atom:Na 1.0 0.00000 0.00000 0.000000 + } +} # NaIon + + +ClIon { + write_once("In Settings") { + pair_coeff @atom:Cl @atom:Cl lj/charmm/coul/long 0.0127850 2.711 + } + + write_once("Data Masses") { + @atom:Cl 35.453 + } + + # assumes "full" atom style + write("Data Atoms") { + $atom:Cl $mol @atom:Cl -1.0 0.00000 0.00000 0.000000 + } +} # ClIon + + +write_once("In Init") { + # -- Default styles for ions -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + kspace_style pppm 0.0001 + pair_modify mix arithmetic +} + +# Optional: Define a group named "ions" consisting of either Na or Cl ions. +write_once("In Settings") { + group ionNa type @atom:NaIon/Na @atom:NaIon/Na + group ionCl type @atom:ClIon/Cl @atom:ClIon/Cl + group ions type @atom:NaIon/Na @atom:ClIon/Cl +} + diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt new file mode 100644 index 000000000..019911c19 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt @@ -0,0 +1,52 @@ +# file "spce.lt" +# +# H1 H2 +# \ / +# O + +SPCE { + + write_once("In Init") { + # -- Default styles (for solo "SPCE" water) -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 + $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 + } + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 1000.0 1.0 + angle_coeff @angle:HOH harmonic 1000.0 109.47 + pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + group spce type @atom:O @atom:H + fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fShakeSPCE during minimization.) + } + +} # end of definition of "SPCE" water molecule type + diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt new file mode 100644 index 000000000..f43f4263e --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt @@ -0,0 +1,52 @@ +import "spce.lt" # <- This defines the SPCE water molecule. This file is + # located in the "common" directory. You can either copy it + # here, or (preferably), you can define a MOLTEMPLATE_PATH + # environment variable and point it to "common". + # (as explained in the installation section of the manual). + +import "ions.lt" # <- This defines the ions "NaIon" and "ClIon". + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 34.50 xlo xhi + 0.0 34.50 ylo yhi + 0.0 34.50 zlo zhi +} + + +# The next command generates a (rather dense) cubic lattice with +# spacing 3.45 Angstroms. (The pressure must be equilibrated later.) + +wat = new SPCE [10].move(0.00, 0.00, 3.45) + [10].move(0.00, 3.45, 0.00) + [10].move(3.45, 0.00, 0.00) + +# We now create a 2x2x2 lattice of Na+ and Cl- ions: + +na = new NaIon [2].move(0,0,17.25) + [2].move(0,17.25,0) + [2].move(17.25,0,0) + + +cl = new ClIon [2].move(0,0,17.25) + [2].move(0,17.25,0) + [2].move(17.25,0,0) + +na[*][*][*].move(5.175,5.175,5.6) +cl[*][*][*].move(12.075,12.075,12.5) + +# (The (5.175,5.175,5.175) and (12.075,12.075,12.075) translational shifts +# prevent the Na and Cl ions from overlapping +# with the water molecules or each other.) + + +# Comment: Fortunately the ions and the water in this example share the +# same force-field styles (so their was no need to use "hybrid" styles). +# If this were not the case, you might need to add something like this. +# +# write_once("In Init") { +# # -- Styles for the combined system (overrides earlier settings) -- +# pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 NEWPAIRSTYLE +# bond_style hybrid harmonic NEWBONDSTYLE +# angle_style hybrid harmonic NEWANGLESTYLE +# } diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt new file mode 100644 index 000000000..4d8af42b5 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt @@ -0,0 +1,48 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- + +# Note: The minimization step is not necessary in this example. However +# in general, it's always a good idea to minimize the system beforehand. +# fShakeSPCE was defined in system.in.settings. It is incompatible with "minimize". +unfix fShakeSPCE +minimize 1.0e-3 1.0e-5 100000 400000 +# Now read "system.in.settings" in order to redefine fShakeSPCE again: +include system.in.settings + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 +thermo 100 + +run 10000 + +# Now that the system's temperature has become more equilibrated, +# we can increase the timestep: + +timestep 2.0 +run 50000 + +write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt new file mode 100644 index 000000000..22fb1f271 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt @@ -0,0 +1,58 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_npt.data + + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- +# Note: If you are reading the restart file instead of the data file, +# then you should not need to minimize the system beforehand.. +# fShakeSPCE was defined in system.in.settings. +# (It is incompatible with "minimize".) +unfix fShakeSPCE +minimize 1.0e-5 1.0e-7 100000 400000 +# Now read "system.in.settings" in order to redefine fShakeSPCE again: +include system.in.settings + +# -- simulation protocol -- + + + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 +thermo 500 + +run 10000 + +# Now that the system's temperature has become more equilibrated, +# we can increase the timestep: + +timestep 2.0 +run 50000 + +write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README.TXT b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README.TXT new file mode 100644 index 000000000..76caac02c --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README.TXT @@ -0,0 +1,22 @@ + Description: + +This is a simulation of pyramid-shaped objects resting on an immobile surface +(resembling graphene). Each pyramid is built from spherical particles stacked +like cannon-balls, or stacked fruit. Ordinarily, the stack does not move +because the particles at the ground layer are immobilized. However, +given an initial (small) perturbation the pyramids collapse in an avalanche. + +(In this example, the perturbation is due to shock because we (intentionally) + did not minimize the system before starting the simulation. This shock + causes an avalanche to occur approximately 5000 timesteps later.) + +The particles roll down the pyramid and bounce off the "ground". The bouncing +is due to a repulsive external force which is added artificially. +(See the "run.in" file.) The simulation looks weird without something +to bounce off of. So I added a graphene surface at the bottom as scenery. +(It does not exert any force on the atoms.) + +(Random comment: This could be a fun example to illustrate the Boltzmann + distribution. Because there is no damping, in a small region, the particle + heights should eventually approach the Boltzmann distribution for some + suitable temperature.) diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_VMD_graphene.txt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_VMD_graphene.txt new file mode 100644 index 000000000..096674f7f --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_VMD_graphene.txt @@ -0,0 +1,28 @@ + ------- A note on building the graphene sheet in VMD: ------ + +Probably you can ignore these instructions. +These instructions are not necessary for this example to run. + +This example contains several pyramid shaped objects resting on a surface +made of graphene. The instructions in this file explain how to build the +graphene (representing the "ground") using VMD instead of with moltemplate. + Why do this? +VMD can create graphene sheets with bonds connecting neighboring carbon atoms, +(which looks more pretty). However, as of 2013-4-29, moltemplate currently +can not generate these bonds. It does not matter physically in this case, +because the graphene sheet used here does not move. It is only used as +scenery, to graphically represent the ground surface. + +Select "Extensions"->"Modeling"->"Carbon Nanotube Builder" + Build a graphene sheet of size 39.8 x 39.8 (units: nm) + 400.3358398 399.876008 + (try to use a size compatible with the periodic boundaries) +Select "Extensions"->"Tk Console", and type + display backgroundgradient on + +Note: If you want to do this, before you run moltemplate, you may want to delete + the sections of the "system.lt" file (located in "moltemplate_files") + which define the graphene wall. Instead create the graphene data file + in VMD. You will have to manually merge the data file for graphene + with the data file for the pyramids created by moltemplate, + (taking care to avoid overlapping atom-id numbers). diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_setup.sh b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_setup.sh new file mode 100755 index 000000000..acc5fbbaa --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_visualize.txt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_visualize.txt new file mode 100644 index 000000000..10198fc92 --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_visualize.txt @@ -0,0 +1,76 @@ + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + To shift the box by a fraction in the x direction (for example) + do this: + + pbc wrap -compound res -all -shiftcenterrel {-0.50 -0.52 0.0 } + pbc box -shiftcenterrel {-0.50 -0.52 0.0 } + + # Alternately if you have a solute whose atoms are all of type 1, + # then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=04800steps_LR.jpg b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=04800steps_LR.jpg new file mode 100644 index 000000000..dc010258f Binary files /dev/null and b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=04800steps_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=12200steps_LR.jpg b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=12200steps_LR.jpg new file mode 100644 index 000000000..53dc98f3e Binary files /dev/null and b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=12200steps_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=33000steps_LR.jpg b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=33000steps_LR.jpg new file mode 100644 index 000000000..ba07b2537 Binary files /dev/null and b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=33000steps_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/README.sh b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/README.sh new file mode 100644 index 000000000..365ab9fb0 --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/README.sh @@ -0,0 +1,15 @@ +# This directory contains moltemplate files for the "Pyramids of Giza" example. +# (Note: the ground lattice work that appears in some images was not generated +# by moltemplate. Moltemplate can not currently create bonded periodic +# structures as of 2013-4-04. Those were generated by topotools.) +# +# To run moltemplate, use: + +moltemplate.sh system.lt + +# This will generate:system.data, system.in, system.in.init, system.in.settings +# +# The output_ttree/ directory will contain files like "Data Atoms", "Data Bonds" +# which contain the corresponding structures of the system.data file. +# (This might make it slightly easier to combine them with atom data and +# bond data generated by other programs, such as topotools, for example.) diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene.lt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene.lt new file mode 100644 index 000000000..3b3e21333 --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene.lt @@ -0,0 +1,61 @@ +# This file contains a unit cell for building graphene and nanotubes +# +# +# The 4AtomRectCellXY "molecule" defined below is a reactangular unit cell +# for hexagonal tesselations in 2-dimensions. (See "graphene_unit_cell.jpg") +# Surfaces constructed with this unit cell can be flat or curved into tubes. +# The distance between nearest-neighbor carbon atoms (ie the length of a +# carbon-carbon bond) is equal to "d" which I set to 1.42 Angstroms. +# +# d = length of each hexagon's side = 1.42 Angstroms +# L = length of each hexagon = 2*d = 2.84 Angstroms +# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478056 Angstroms +# 2w = width of hexagon rows = 3*l = 4.26 Angstroms +# +# Consequently, the Lattice-cell vectors for singe-layer graphene are: +# (2.4595121467478, 0, 0) (aligned with X axis) +# (0, 4.26, 0) (aligned with Y axis) +# So, to build a sheet of graphite, you could use: +# sheet = new Graphene/4AtomRectCellXY [10].move(2.4595121467478, 0, 0) +# [10].move(0, 4.26, 0) + + + + +Graphene { + + 4AtomRectCellXY + { + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom:C11 $mol:... @atom:../C 0.0 0.61487803668695 0.71 0.0 + $atom:C21 $mol:... @atom:../C 0.0 1.84463411006085 1.42 0.0 + $atom:C12 $mol:... @atom:../C 0.0 0.61487803668695 3.55 0.0 + $atom:C22 $mol:... @atom:../C 0.0 1.84463411006085 2.84 0.0 + } + } + + # Now define properties of the Carbon graphene atom + + write_once("In Init") { + pair_style hybrid lj/cut 9.0 + } + + write_once("Data Masses") { + @atom:C 12.0 + } + + write_once("In Settings") { + # i j epsilon sigma + pair_coeff @atom:C @atom:C lj/cut 0.068443 3.407 + + # These Lennard-Jones parameters come from + # R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus, + # Chem Phys Lett, 348:187 (2001) + + # Define a group consisting of only carbon atoms in graphene molecules + group gGraphene type @atom:C + } + +} # Graphene + diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene_wall.lt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene_wall.lt new file mode 100644 index 000000000..759f0f5d0 --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene_wall.lt @@ -0,0 +1,21 @@ +import "graphene.lt" + +# -------------- graphene sheet ----------------- + +# Notes: +# Hexagonal lattice with: +# l = length of each hexagonal side = 1.42 Angstroms +# L = length of each hexagon = 2*l = 2.84 Angstroms +# W = width of each hexagon = 2*l*sqrt(3)/2 ~= 2.4595121467478 Angstroms +# 2w = width of hexagon rows = 3.0*l = 4.26 Angstroms + + +GrapheneWall { + + unitcells = new Graphene/4AtomRectCellXY [163].move(2.456, 0, 0) + [94].move(0, 4.254, 0) + + # (Note: I fudged the spacing slightly to make it line up better with the + # lattice spacing for graphene generated by VMD's graphene builder.) +} + diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/pyramids.lt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/pyramids.lt new file mode 100644 index 000000000..84c2b6f6d --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/pyramids.lt @@ -0,0 +1,283 @@ +# Brick is a very simple molecule containing one "atom". +# "ImmobileBrick" and "GoldBrick" are identical to "Brick" but are +# given different atom types. (This makes it easier to put them in +# different groups and apply different LAMMPS "fixes" to them.) + +Brick { + + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom $mol @atom 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom 1.0 + } + + write_once("In Settings") { + # U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6) + # + # i j eps sig + pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393 + } + + write_once("In Settings") { + group gMobile type @atom + # (Atoms of this type belong to the "gMobile" group) + } + + write_once("In Init") { + atom_style full + units lj + pair_style lj/cut 1.0 + } +} + + + +#We want to stack "Brick"s the same way a green-grocer sometimes stack apples: +#Place the apples at the base an square lattice of apples at the base. +#The apples in the next layer up are placed in between the 4 apples beneath them. +#Each new layer is smaller and placed above the previous layer at a height +#of sigma / sqrt(2), where "sigma" is the diameter of each spherical "Brick". +#We will artificially hold the apples at the base in place +#(to keep the entire stack from collapsing). +# +# The lines below were generated from the following python loop: +# +#from math import * +#N=50 +#s=1.0 +#for i in range(0,N): +# print(" layer"+str(i)+" = new Brick.move("+str(-(N-(i+1))*s*0.5)+","+ +# str(-(N-(i+1))*s*0.5)+","+str(i*s/sqrt(2))+") ["+str(N-i)+"].move("+ +# str(s)+",0,0) ["+str(N-i)+"].move(0,"+str(s)+",0)") + + +PyramidKhufu { + layer0 = new ImmobileBrick.move(-24.5,-24.5,0.0) [50].move(1.0,0,0) [50].move(0,1.0,0) + layer1 = new Brick.move(-24.0,-24.0,0.707106781187) [49].move(1.0,0,0) [49].move(0,1.0,0) + layer2 = new Brick.move(-23.5,-23.5,1.41421356237) [48].move(1.0,0,0) [48].move(0,1.0,0) + layer3 = new Brick.move(-23.0,-23.0,2.12132034356) [47].move(1.0,0,0) [47].move(0,1.0,0) + layer4 = new Brick.move(-22.5,-22.5,2.82842712475) [46].move(1.0,0,0) [46].move(0,1.0,0) + layer5 = new Brick.move(-22.0,-22.0,3.53553390593) [45].move(1.0,0,0) [45].move(0,1.0,0) + layer6 = new Brick.move(-21.5,-21.5,4.24264068712) [44].move(1.0,0,0) [44].move(0,1.0,0) + layer7 = new Brick.move(-21.0,-21.0,4.94974746831) [43].move(1.0,0,0) [43].move(0,1.0,0) + layer8 = new Brick.move(-20.5,-20.5,5.65685424949) [42].move(1.0,0,0) [42].move(0,1.0,0) + layer9 = new Brick.move(-20.0,-20.0,6.36396103068) [41].move(1.0,0,0) [41].move(0,1.0,0) + layer10 = new Brick.move(-19.5,-19.5,7.07106781187) [40].move(1.0,0,0) [40].move(0,1.0,0) + layer11 = new Brick.move(-19.0,-19.0,7.77817459305) [39].move(1.0,0,0) [39].move(0,1.0,0) + layer12 = new Brick.move(-18.5,-18.5,8.48528137424) [38].move(1.0,0,0) [38].move(0,1.0,0) + layer13 = new Brick.move(-18.0,-18.0,9.19238815543) [37].move(1.0,0,0) [37].move(0,1.0,0) + layer14 = new Brick.move(-17.5,-17.5,9.89949493661) [36].move(1.0,0,0) [36].move(0,1.0,0) + layer15 = new Brick.move(-17.0,-17.0,10.6066017178) [35].move(1.0,0,0) [35].move(0,1.0,0) + layer16 = new Brick.move(-16.5,-16.5,11.313708499) [34].move(1.0,0,0) [34].move(0,1.0,0) + layer17 = new Brick.move(-16.0,-16.0,12.0208152802) [33].move(1.0,0,0) [33].move(0,1.0,0) + layer18 = new Brick.move(-15.5,-15.5,12.7279220614) [32].move(1.0,0,0) [32].move(0,1.0,0) + layer19 = new Brick.move(-15.0,-15.0,13.4350288425) [31].move(1.0,0,0) [31].move(0,1.0,0) + layer20 = new Brick.move(-14.5,-14.5,14.1421356237) [30].move(1.0,0,0) [30].move(0,1.0,0) + layer21 = new Brick.move(-14.0,-14.0,14.8492424049) [29].move(1.0,0,0) [29].move(0,1.0,0) + layer22 = new Brick.move(-13.5,-13.5,15.5563491861) [28].move(1.0,0,0) [28].move(0,1.0,0) + layer23 = new Brick.move(-13.0,-13.0,16.2634559673) [27].move(1.0,0,0) [27].move(0,1.0,0) + layer24 = new Brick.move(-12.5,-12.5,16.9705627485) [26].move(1.0,0,0) [26].move(0,1.0,0) + layer25 = new Brick.move(-12.0,-12.0,17.6776695297) [25].move(1.0,0,0) [25].move(0,1.0,0) + layer26 = new Brick.move(-11.5,-11.5,18.3847763109) [24].move(1.0,0,0) [24].move(0,1.0,0) + layer27 = new Brick.move(-11.0,-11.0,19.091883092) [23].move(1.0,0,0) [23].move(0,1.0,0) + layer28 = new Brick.move(-10.5,-10.5,19.7989898732) [22].move(1.0,0,0) [22].move(0,1.0,0) + layer29 = new Brick.move(-10.0,-10.0,20.5060966544) [21].move(1.0,0,0) [21].move(0,1.0,0) + layer30 = new Brick.move(-9.5,-9.5,21.2132034356) [20].move(1.0,0,0) [20].move(0,1.0,0) + layer31 = new Brick.move(-9.0,-9.0,21.9203102168) [19].move(1.0,0,0) [19].move(0,1.0,0) + layer32 = new Brick.move(-8.5,-8.5,22.627416998) [18].move(1.0,0,0) [18].move(0,1.0,0) + layer33 = new Brick.move(-8.0,-8.0,23.3345237792) [17].move(1.0,0,0) [17].move(0,1.0,0) + layer34 = new Brick.move(-7.5,-7.5,24.0416305603) [16].move(1.0,0,0) [16].move(0,1.0,0) + layer35 = new Brick.move(-7.0,-7.0,24.7487373415) [15].move(1.0,0,0) [15].move(0,1.0,0) + layer36 = new Brick.move(-6.5,-6.5,25.4558441227) [14].move(1.0,0,0) [14].move(0,1.0,0) + layer37 = new Brick.move(-6.0,-6.0,26.1629509039) [13].move(1.0,0,0) [13].move(0,1.0,0) + layer38 = new Brick.move(-5.5,-5.5,26.8700576851) [12].move(1.0,0,0) [12].move(0,1.0,0) + layer39 = new Brick.move(-5.0,-5.0,27.5771644663) [11].move(1.0,0,0) [11].move(0,1.0,0) + layer40 = new GoldBrick.move(-4.5,-4.5,28.2842712475) [10].move(1.0,0,0) [10].move(0,1.0,0) + layer41 = new GoldBrick.move(-4.0,-4.0,28.9913780286) [9].move(1.0,0,0) [9].move(0,1.0,0) + layer42 = new GoldBrick.move(-3.5,-3.5,29.6984848098) [8].move(1.0,0,0) [8].move(0,1.0,0) + layer43 = new GoldBrick.move(-3.0,-3.0,30.405591591) [7].move(1.0,0,0) [7].move(0,1.0,0) + layer44 = new GoldBrick.move(-2.5,-2.5,31.1126983722) [6].move(1.0,0,0) [6].move(0,1.0,0) + layer45 = new GoldBrick.move(-2.0,-2.0,31.8198051534) [5].move(1.0,0,0) [5].move(0,1.0,0) + layer46 = new GoldBrick.move(-1.5,-1.5,32.5269119346) [4].move(1.0,0,0) [4].move(0,1.0,0) + layer47 = new GoldBrick.move(-1.0,-1.0,33.2340187158) [3].move(1.0,0,0) [3].move(0,1.0,0) + layer48 = new GoldBrick.move(-0.5,-0.5,33.941125497) [2].move(1.0,0,0) [2].move(0,1.0,0) + layer49 = new GoldBrick.move(0.0,0.0,34.6482322781) [1].move(1.0,0,0) [1].move(0,1.0,0) +} + + +PyramidKhafre { + layer0 = new ImmobileBrick.move(-23.5,-23.5,0.0) [48].move(1.0,0,0) [48].move(0,1.0,0) + layer1 = new Brick.move(-23.0,-23.0,0.707106781187) [47].move(1.0,0,0) [47].move(0,1.0,0) + layer2 = new Brick.move(-22.5,-22.5,1.41421356237) [46].move(1.0,0,0) [46].move(0,1.0,0) + layer3 = new Brick.move(-22.0,-22.0,2.12132034356) [45].move(1.0,0,0) [45].move(0,1.0,0) + layer4 = new Brick.move(-21.5,-21.5,2.82842712475) [44].move(1.0,0,0) [44].move(0,1.0,0) + layer5 = new Brick.move(-21.0,-21.0,3.53553390593) [43].move(1.0,0,0) [43].move(0,1.0,0) + layer6 = new Brick.move(-20.5,-20.5,4.24264068712) [42].move(1.0,0,0) [42].move(0,1.0,0) + layer7 = new Brick.move(-20.0,-20.0,4.94974746831) [41].move(1.0,0,0) [41].move(0,1.0,0) + layer8 = new Brick.move(-19.5,-19.5,5.65685424949) [40].move(1.0,0,0) [40].move(0,1.0,0) + layer9 = new Brick.move(-19.0,-19.0,6.36396103068) [39].move(1.0,0,0) [39].move(0,1.0,0) + layer10 = new Brick.move(-18.5,-18.5,7.07106781187) [38].move(1.0,0,0) [38].move(0,1.0,0) + layer11 = new Brick.move(-18.0,-18.0,7.77817459305) [37].move(1.0,0,0) [37].move(0,1.0,0) + layer12 = new Brick.move(-17.5,-17.5,8.48528137424) [36].move(1.0,0,0) [36].move(0,1.0,0) + layer13 = new Brick.move(-17.0,-17.0,9.19238815543) [35].move(1.0,0,0) [35].move(0,1.0,0) + layer14 = new Brick.move(-16.5,-16.5,9.89949493661) [34].move(1.0,0,0) [34].move(0,1.0,0) + layer15 = new Brick.move(-16.0,-16.0,10.6066017178) [33].move(1.0,0,0) [33].move(0,1.0,0) + layer16 = new Brick.move(-15.5,-15.5,11.313708499) [32].move(1.0,0,0) [32].move(0,1.0,0) + layer17 = new Brick.move(-15.0,-15.0,12.0208152802) [31].move(1.0,0,0) [31].move(0,1.0,0) + layer18 = new Brick.move(-14.5,-14.5,12.7279220614) [30].move(1.0,0,0) [30].move(0,1.0,0) + layer19 = new Brick.move(-14.0,-14.0,13.4350288425) [29].move(1.0,0,0) [29].move(0,1.0,0) + layer20 = new Brick.move(-13.5,-13.5,14.1421356237) [28].move(1.0,0,0) [28].move(0,1.0,0) + layer21 = new Brick.move(-13.0,-13.0,14.8492424049) [27].move(1.0,0,0) [27].move(0,1.0,0) + layer22 = new Brick.move(-12.5,-12.5,15.5563491861) [26].move(1.0,0,0) [26].move(0,1.0,0) + layer23 = new Brick.move(-12.0,-12.0,16.2634559673) [25].move(1.0,0,0) [25].move(0,1.0,0) + layer24 = new Brick.move(-11.5,-11.5,16.9705627485) [24].move(1.0,0,0) [24].move(0,1.0,0) + layer25 = new Brick.move(-11.0,-11.0,17.6776695297) [23].move(1.0,0,0) [23].move(0,1.0,0) + layer26 = new Brick.move(-10.5,-10.5,18.3847763109) [22].move(1.0,0,0) [22].move(0,1.0,0) + layer27 = new Brick.move(-10.0,-10.0,19.091883092) [21].move(1.0,0,0) [21].move(0,1.0,0) + layer28 = new Brick.move(-9.5,-9.5,19.7989898732) [20].move(1.0,0,0) [20].move(0,1.0,0) + layer29 = new Brick.move(-9.0,-9.0,20.5060966544) [19].move(1.0,0,0) [19].move(0,1.0,0) + layer30 = new Brick.move(-8.5,-8.5,21.2132034356) [18].move(1.0,0,0) [18].move(0,1.0,0) + layer31 = new Brick.move(-8.0,-8.0,21.9203102168) [17].move(1.0,0,0) [17].move(0,1.0,0) + layer32 = new Brick.move(-7.5,-7.5,22.627416998) [16].move(1.0,0,0) [16].move(0,1.0,0) + layer33 = new Brick.move(-7.0,-7.0,23.3345237792) [15].move(1.0,0,0) [15].move(0,1.0,0) + layer34 = new Brick.move(-6.5,-6.5,24.0416305603) [14].move(1.0,0,0) [14].move(0,1.0,0) + layer35 = new GoldBrick.move(-6.0,-6.0,24.7487373415) [13].move(1.0,0,0) [13].move(0,1.0,0) + layer36 = new GoldBrick.move(-5.5,-5.5,25.4558441227) [12].move(1.0,0,0) [12].move(0,1.0,0) + layer37 = new GoldBrick.move(-5.0,-5.0,26.1629509039) [11].move(1.0,0,0) [11].move(0,1.0,0) + layer38 = new GoldBrick.move(-4.5,-4.5,26.8700576851) [10].move(1.0,0,0) [10].move(0,1.0,0) + layer39 = new GoldBrick.move(-4.0,-4.0,27.5771644663) [9].move(1.0,0,0) [9].move(0,1.0,0) + layer40 = new GoldBrick.move(-3.5,-3.5,28.2842712475) [8].move(1.0,0,0) [8].move(0,1.0,0) + layer41 = new GoldBrick.move(-3.0,-3.0,28.9913780286) [7].move(1.0,0,0) [7].move(0,1.0,0) + layer42 = new GoldBrick.move(-2.5,-2.5,29.6984848098) [6].move(1.0,0,0) [6].move(0,1.0,0) + layer43 = new GoldBrick.move(-2.0,-2.0,30.405591591) [5].move(1.0,0,0) [5].move(0,1.0,0) + layer44 = new GoldBrick.move(-1.5,-1.5,31.1126983722) [4].move(1.0,0,0) [4].move(0,1.0,0) + layer45 = new GoldBrick.move(-1.0,-1.0,31.8198051534) [3].move(1.0,0,0) [3].move(0,1.0,0) + layer46 = new GoldBrick.move(-0.5,-0.5,32.5269119346) [2].move(1.0,0,0) [2].move(0,1.0,0) + layer47 = new GoldBrick.move(0.0,0.0,33.2340187158) [1].move(1.0,0,0) [1].move(0,1.0,0) +} + + +PyramidMenkaure { + layer0 = new ImmobileBrick.move(-9.0,-9.0,0.0) [19].move(1.0,0,0) [19].move(0,1.0,0) + layer1 = new Brick.move(-8.5,-8.5,0.707106781187) [18].move(1.0,0,0) [18].move(0,1.0,0) + layer2 = new Brick.move(-8.0,-8.0,1.41421356237) [17].move(1.0,0,0) [17].move(0,1.0,0) + layer3 = new Brick.move(-7.5,-7.5,2.12132034356) [16].move(1.0,0,0) [16].move(0,1.0,0) + layer4 = new Brick.move(-7.0,-7.0,2.82842712475) [15].move(1.0,0,0) [15].move(0,1.0,0) + layer5 = new Brick.move(-6.5,-6.5,3.53553390593) [14].move(1.0,0,0) [14].move(0,1.0,0) + layer6 = new Brick.move(-6.0,-6.0,4.24264068712) [13].move(1.0,0,0) [13].move(0,1.0,0) + layer7 = new Brick.move(-5.5,-5.5,4.94974746831) [12].move(1.0,0,0) [12].move(0,1.0,0) + layer8 = new Brick.move(-5.0,-5.0,5.65685424949) [11].move(1.0,0,0) [11].move(0,1.0,0) + layer9 = new Brick.move(-4.5,-4.5,6.36396103068) [10].move(1.0,0,0) [10].move(0,1.0,0) + layer10 = new Brick.move(-4.0,-4.0,7.07106781187) [9].move(1.0,0,0) [9].move(0,1.0,0) + layer11 = new Brick.move(-3.5,-3.5,7.77817459305) [8].move(1.0,0,0) [8].move(0,1.0,0) + layer12 = new Brick.move(-3.0,-3.0,8.48528137424) [7].move(1.0,0,0) [7].move(0,1.0,0) + layer13 = new Brick.move(-2.5,-2.5,9.19238815543) [6].move(1.0,0,0) [6].move(0,1.0,0) + layer14 = new Brick.move(-2.0,-2.0,9.89949493661) [5].move(1.0,0,0) [5].move(0,1.0,0) + layer15 = new Brick.move(-1.5,-1.5,10.6066017178) [4].move(1.0,0,0) [4].move(0,1.0,0) + layer16 = new Brick.move(-1.0,-1.0,11.313708499) [3].move(1.0,0,0) [3].move(0,1.0,0) + layer17 = new Brick.move(-0.5,-0.5,12.0208152802) [2].move(1.0,0,0) [2].move(0,1.0,0) + layer18 = new Brick.move(0.0,0.0,12.7279220614) [1].move(1.0,0,0) [1].move(0,1.0,0) +} + +PyramidQueens1 { + layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0) + layer1 = new ImmobileBrick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0) + layer2 = new ImmobileBrick.move(-2.0,-2.0,1.707106781187) [5].move(1.0,0,0) [5].move(0,1.0,0) + layer3 = new Brick.move(-1.5,-1.5,2.41421356237) [4].move(1.0,0,0) [4].move(0,1.0,0) + layer4 = new Brick.move(-0.5,-0.5,3.41421356237) [2].move(1.0,0,0) [2].move(0,1.0,0) + layer5 = new Brick.move(0.0,0.0,4.12132034356) [1].move(1.0,0,0) [1].move(0,1.0,0) +} + +PyramidQueens2 { + layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0) + layer1 = new ImmobileBrick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0) + layer2 = new ImmobileBrick.move(-2.0,-2.0,1.707106781187) [5].move(1.0,0,0) [5].move(0,1.0,0) + layer3 = new Brick.move(-1.5,-1.5,2.41421356237) [4].move(1.0,0,0) [4].move(0,1.0,0) + layer4 = new Brick.move(-0.5,-0.5,3.41421356237) [2].move(1.0,0,0) [2].move(0,1.0,0) + layer5 = new Brick.move(0.0,0.0,4.12132034356) [1].move(1.0,0,0) [1].move(0,1.0,0) +} + +PyramidQueens3 { + layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0) + layer1 = new Brick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0) + layer2 = new Brick.move(-2.5,-2.5,1.41421356237) [6].move(1.0,0,0) [6].move(0,1.0,0) + layer3 = new Brick.move(-2.0,-2.0,2.12132034356) [5].move(1.0,0,0) [5].move(0,1.0,0) + layer4 = new Brick.move(-1.5,-1.5,2.82842712475) [4].move(1.0,0,0) [4].move(0,1.0,0) + layer5 = new Brick.move(-1.0,-1.0,3.53553390593) [3].move(1.0,0,0) [3].move(0,1.0,0) + layer6 = new Brick.move(-0.5,-0.5,4.24264068712) [2].move(1.0,0,0) [2].move(0,1.0,0) + layer7 = new Brick.move(0.0,0.0,4.94974746831) [1].move(1.0,0,0) [1].move(0,1.0,0) +} + + + + +# "ImmobileBrick"s are identical to "Brick"s, +# except that they have a different atom type. +# We can define groups based on atom type +# and apply fixes to them. + +ImmobileBrick { + + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom $mol @atom 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom 1.0 + } + + write_once("In Settings") { + # U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6) + # + # i j eps sig + pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393 + } + + write_once("In Settings") { + group gImmobile type @atom + # (Atoms of this type belong to the "gImmobile" group) + } + + write_once("In Init") { + atom_style full + units lj + pair_style hybrid lj/cut 1.0 + } +} + + + +GoldBrick { + + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom $mol @atom 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom 1.0 + } + + write_once("In Settings") { + # U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6) + # + # i j eps sig + pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393 + } + + write_once("In Settings") { + group gMobile type @atom + # (Atoms of this type belong to the "gMobile" group) + } + + write_once("In Init") { + atom_style full + units lj + pair_style lj/cut 1.0 + } +} + diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/system.lt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/system.lt new file mode 100644 index 000000000..0c9c50ae9 --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/system.lt @@ -0,0 +1,80 @@ +# Description. +# This is a simulation of pyramid-like objects made of particles stacked +# and arranged like cannon-balls, or fruit-stands. Ordinarilly, the stack +# does not collapse because the particles at the ground layer are immobilized. +# However given an initial perterbation the pyramids collapse in an avalanche. +# (This can happen, for example when you do not minimize the system beforehand.) +# The particles roll down the pyramid and bounce off the "ground". The bouncing +# is due to a repulsive external force which is added artificially. +# (See the "run.in" file.) The simulation looks weird without something +# to bounce off of. So I added a graphene surface at the bottom as scenery. +# The ground does not serve any purpose except to look pretty. +# +# (Because there is no damping, I suspect that the distribution of heights of +# the particles in a small area should approach the Boltzmann distribution, +# if you run the simulation long enough.) + + +# ----------------- Pyramids: ----------------- + +import "pyramids.lt" + +# Move the pyramids into their locations in Giza (approximate) + +pyramidKhufu = new PyramidKhufu.move(210, 215, 1) +pyramidKhafre = new PyramidKhafre.move(150, 150, 1) +pyramidMenkaure = new PyramidMenkaure.move(105, 082, 1) +PyramidQueens1 = new PyramidQueens1.move(089, 059, 1) +PyramidQueens2 = new PyramidQueens2.move(100, 059, 1) +PyramidQueens3 = new PyramidQueens3.move(111, 059, 1) + + +# --------------- Scenery: -------------------- + +import "graphene_wall.lt" + +graphene_wall = new GrapheneWall + +write_once("In Settings") { + # Turn off all interactions with the graphene atoms by setting epsilon to 0. + # (We will use a different repulsive barrier to represent the ground instead.) + # These atoms are just "for show". epsilon sigma + pair_coeff @atom:Graphene/C @atom:Graphene/C lj/cut 0.00000 3.407 + + # Optional: Add the graphene atoms to the "gImmobile" group. Later freeze them + group gImmobile type @atom:Graphene/C +} + +# Unfortunately, the ground still looks kind of ugly because moltemplate does +# not yet know how to automatically connect nearby carbon atoms with C-C bonds +# (based on distance). (As of 2013-4-29, moltemplate is not good at +# generating crystalline objects containing explicit bonds.) +# If you want bonds between atoms, use VMD's "carbon-nanotube-builder plugin" +# (which creates data files with bonds) and then merge the two data files +# manually later. (This is not done here.) + + +# -------- override earlier settings ---------- + +write_once("In Init") { + # Override any earlier style settings + atom_style full + units lj + pair_style hybrid lj/cut 1.0 + bond_style none + angle_style none + dihedral_style none + improper_style none + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 0.0 +} + +# ------------ boundary conditions ------------ + +write_once("Data Boundary") { + -1.842033 398.493813 xlo xhi + -0.708994 399.167013 ylo yhi + 0.0 400.0 zlo zhi +} +# --------------------------------------------- + diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/run.in b/tools/moltemplate/examples/silly/pyramids_vs_gravity/run.in new file mode 100644 index 000000000..4feec9ff4 --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/run.in @@ -0,0 +1,64 @@ +# -- Init Section -- + +include system.in.init +boundary p p f + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.0025 +dump 1 all custom 200 traj_nvt.lammpstrj id mol type x y z ix iy iz + +thermo_style custom step temp pe etotal +thermo 100 # time interval for printing out "thermo" data + +# ---- Set up the physical environment ---- + +# Add gravity: +fix fxGrav gMobile gravity 0.05 vector 0 0 -1 + +# Create a "ground" surface. +# This is a repulsive "wall" which particles can bounce off of: + +fix fxWall gMobile wall/lj126 zlo EDGE 1.0 0.8908987181403393 1.0 + + +# ---- Evolve the system: ---- + +# Evolve the (mobile) atoms using ordinary Newton's laws (NVE) + +fix fxNVE gMobile nve + + +# IF YOU WANT TO ADD DAMPING, THEN UNCOMMENT THE NEXT LINE: +#fix fxLan gMobile langevin 0.001 0.001 10000.0 48279 +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve" +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) +# This was not tested. + +# For efficient simulation in parallel, try using "fix balance": +# (This will adjust the spatial decomposition as the distribution of +# particles changes over time.) + +fix fxBalance gMobile balance 1000 xy 20 1.3 + +# Optional: Improve efficiency by omitting the calcuation of interactions +# between immobile atoms: + +neigh_modify exclude group gImmobile gImmobile + + +restart 50000 restart_nvt + +run 200000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/silly/sierpinski/README.TXT b/tools/moltemplate/examples/silly/sierpinski/README.TXT new file mode 100644 index 000000000..6bc152b18 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/README.TXT @@ -0,0 +1,45 @@ +NOTE: This example requires the "Al99.eam.alloy" file. + (It was not included in this directory because if its large size.) + As of 2012-11, I was able to obtain it here: + http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy + Copy it to the directory containing this README file. +------------------------------------------------------------------------ +3D fractal test + +Moltemplate is useful for building larger molecular structures from +smaller pieces. Although this simulation is of no scientific value, thiss +example illustrates how to build large (many-level) heirarchical objects +(Serpinski cubes) using moltemplate. (This is also called a "Menger Sponge".) + +The files in this directory demonstrate a way to build a periodic lattice of +3-dimensional Serpinski-cubes (with 3 levels of recursive self-similarity). + +In this example, the basic indivisible units are 4-atoms of Aluminum +(arranged in a cubic FCC unit-cell for bulk Aluminum). +This was an arbitrary choice. The resulting construct is not stable. +(But it makes pretty movies while collapsing.) + +To understand what is going on with this example, look at this file: + +./moltemplate_files/elegant_inefficient_version/serpinski_cubes.lt + +(This approach uses too much memory to be practical for large simulaions. +The version I actually use is here: ./moltemplate_files/serpinski_cubes.lt) + + --- To build the system --- + +Carry out the instructions in README_setup.sh, +to generate the LAMMPS DATA file and input scripts you need: +system.data, system.in.init, system.in.settings. +(The run.in script contains references to these files.) + + --- To run LAMMPS, try a command like: --- + +lmp_linux -i run.in + + or (if you have mpi installed) + +mpirun -np 4 lmp_linux -i run.in + +This will create an ordinary LAMMPS dump file you can visualize with VMD +traj.lammpstrj (See README_visualize.txt) diff --git a/tools/moltemplate/examples/silly/sierpinski/README_setup.sh b/tools/moltemplate/examples/silly/sierpinski/README_setup.sh new file mode 100755 index 000000000..2af3d7372 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/README_setup.sh @@ -0,0 +1,29 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -atomstyle full system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # We will also need the "Al99.eam.alloy" file: + #cp -f Al99.eam.alloy ../ + # This file was downloaded from: + # http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy + + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/silly/sierpinski/README_visualize.txt b/tools/moltemplate/examples/silly/sierpinski/README_visualize.txt new file mode 100644 index 000000000..019afc144 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/silly/sierpinski/images/AlCell_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/AlCell_LR.jpg new file mode 100644 index 000000000..bf07914da Binary files /dev/null and b/tools/moltemplate/examples/silly/sierpinski/images/AlCell_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/lvl1_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/lvl1_LR.jpg new file mode 100644 index 000000000..11174969a Binary files /dev/null and b/tools/moltemplate/examples/silly/sierpinski/images/lvl1_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/lvl2_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/lvl2_LR.jpg new file mode 100644 index 000000000..744c9af63 Binary files /dev/null and b/tools/moltemplate/examples/silly/sierpinski/images/lvl2_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/lvl3_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/lvl3_LR.jpg new file mode 100644 index 000000000..a72a1ea8d Binary files /dev/null and b/tools/moltemplate/examples/silly/sierpinski/images/lvl3_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=0_zoom1_LR2.jpg b/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=0_zoom1_LR2.jpg new file mode 100644 index 000000000..9020a3be0 Binary files /dev/null and b/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=0_zoom1_LR2.jpg differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=7400_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=7400_LR.jpg new file mode 100644 index 000000000..0036c903a Binary files /dev/null and b/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=7400_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/al_cell.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/al_cell.lt new file mode 100644 index 000000000..3054a45e0 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/al_cell.lt @@ -0,0 +1,64 @@ +# "AlCell" defines the 4-atom FCC unit cell +# of Aluminum (with a 4.05 angstrom spacing) + +AlCell { + + # AtomID MolID(IGNORE!) AtomType Charge X Y Z + + write("Data Atoms") { + $atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000 + $atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025 + $atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025 + $atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000 + } + + write_once("In Init") { + units metal + atom_style full # <- Requires each atom has a MolID and Charge. + # This is not necessary. (Why use "full"? + # The "full" atom style is useful if you want to + # mix the aluminum with other molecules later. + # Otherwise, just use "atom_style atomic", and + # and remove the 2nd and 4th columns above.) + pair_style eam/alloy + } + + write_once("In Settings") { + pair_coeff * * Al99.eam.alloy Al + } + + write_once("Data Masses") { + @atom:Al 27.0 + } + +} # AlCell + + + + + +# Here is an alternate way to define AlCell +# using "scale(4.05)" to select the lattice spacing: +# +#FccCell { +# write("Data Atoms") { +# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0 +# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5 +# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5 +# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0 +# } +# write_once("Data Masses") { +# @atom:Al 27.0 +# } +# write_once("In Init") { +# units metal +# atom_style full +# pair_style eam/alloy +# } +# write_once("In Settings") { +# pair_coeff * * Al99.eam.alloy Al +# } +#} +# +#AlCell = FccCell.scale(4.05) +# diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/al_cell.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/al_cell.lt new file mode 100644 index 000000000..3054a45e0 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/al_cell.lt @@ -0,0 +1,64 @@ +# "AlCell" defines the 4-atom FCC unit cell +# of Aluminum (with a 4.05 angstrom spacing) + +AlCell { + + # AtomID MolID(IGNORE!) AtomType Charge X Y Z + + write("Data Atoms") { + $atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000 + $atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025 + $atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025 + $atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000 + } + + write_once("In Init") { + units metal + atom_style full # <- Requires each atom has a MolID and Charge. + # This is not necessary. (Why use "full"? + # The "full" atom style is useful if you want to + # mix the aluminum with other molecules later. + # Otherwise, just use "atom_style atomic", and + # and remove the 2nd and 4th columns above.) + pair_style eam/alloy + } + + write_once("In Settings") { + pair_coeff * * Al99.eam.alloy Al + } + + write_once("Data Masses") { + @atom:Al 27.0 + } + +} # AlCell + + + + + +# Here is an alternate way to define AlCell +# using "scale(4.05)" to select the lattice spacing: +# +#FccCell { +# write("Data Atoms") { +# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0 +# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5 +# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5 +# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0 +# } +# write_once("Data Masses") { +# @atom:Al 27.0 +# } +# write_once("In Init") { +# units metal +# atom_style full +# pair_style eam/alloy +# } +# write_once("In Settings") { +# pair_coeff * * Al99.eam.alloy Al +# } +#} +# +#AlCell = FccCell.scale(4.05) +# diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/sierpinski_cubes.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/sierpinski_cubes.lt new file mode 100644 index 000000000..28c2d5ea2 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/sierpinski_cubes.lt @@ -0,0 +1,34 @@ +import "al_cell.lt" # <- defines the 4-atom "AlCell" FCC Aluminum unit cell + +# This approach uses the "delete" command. +# It works and it is elegant, but because the majority of atoms will be +# deleted, (and because memory is allocated for all atoms, including +# deleted atoms) this approach is not very memory efficient. + +SierpinskiCubeLvl1 { + cells = new AlCell [3].move(0.00, 0.00, 4.05) + [3].move(0.00, 4.05, 0.00) + [3].move(4.05, 0.00, 0.00) + delete cells[*][1][1] + delete cells[1][*][1] + delete cells[1][1][*] +} + +SierpinskiCubeLvl2 { + cells = new SierpinskiCubeLvl1 [3].move(0.00, 0.00, 12.15) + [3].move(0.00, 12.15, 0.00) + [3].move(12.15, 0.00, 0.00) + delete cells[*][1][1] + delete cells[1][*][1] + delete cells[1][1][*] +} + +SierpinskiCubeLvl3 { + cells = new SierpinskiCubeLvl2 [3].move(0.00, 0.00, 36.45) + [3].move(0.00, 36.45, 0.00) + [3].move(36.45, 0.00, 0.00) + delete cells[*][1][1] + delete cells[1][*][1] + delete cells[1][1][*] +} + diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/system.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/system.lt new file mode 100644 index 000000000..b14929e98 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/system.lt @@ -0,0 +1,34 @@ +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 72.9 xlo xhi + 0.0 72.9 ylo yhi + 0.0 72.9 zlo zhi +} + +import "sierpinski_cubes.lt" + +cells = new SierpinskiCubeLvl2 [2].move(0.00, 0.00, 36.45) + [2].move(0.00, 36.45, 0.00) + [2].move(36.45, 0.00, 0.00) +delete cells[*][1][1] +delete cells[1][*][1] +delete cells[1][1][*] + + + + + + + + + + + + +################################################################ +# The next command is not necessary: +# + create_var { $mol } # <-This forces all of the Al atoms in the crystal +# # to share the same molecule ID number. +# # Molecule ID numbers are not necessary. Ignore this. +# diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/sierpinski_cubes.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/sierpinski_cubes.lt new file mode 100644 index 000000000..d45a8331b --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/sierpinski_cubes.lt @@ -0,0 +1,66 @@ +import "al_cell.lt" # <- defines the 4-atom "AlCell" FCC Aluminum unit cell + +# A Sierpinski cube resembles a 3x3x3 Rubik's-cube-like object with the smaller +# cube in each central face (and in the interior) removed. There are 3x3x3-7=20 +# remaining sub-cubes. Each of these 20 sub-cubes is a smaller SierpinskiCube. +# To build a SierpinskiCube, you can list all 20 sub-cubes, or you can fill a +# 3x3x3 cube with sub-cubes and delete the interior sub-cubes. (The later +# approach is used in file "elegant_inefficient_version/sierpinski_cubes.lt") + + + +SierpinskiCubeLvl1 { + # Again, a Sierpinski-cube is constructed of 20 smaller cube-shaped objects. + # Here, the small cube-shaped objects are "AlCells" (defined in "al_cell.lt"). + # I could list out the positions of all 20 AlCells, (and this would be clearer + # for the reader). However instead I built it from a combination of + # two-dimensional and three-dimensional arrays of AlCells (explained below). + + # The next command creates 4 AlCells at: (0, 4.05, 0.0), (8.1, 4.05, 0.0), + # (0, 4.05, 8.1), (8.1, 4.05, 8.1) + + cells_xz = new AlCell.move(0.00, 4.05, 0.00) [2].move(8.10, 0.0, 0.0 ) + [2].move(0.0, 0.0, 8.10) + + # The next command creates 4 AlCells at: (4.05, 0, 0.0), (4.05, 8.1, 0.0), + # (4.05, 0, 8.1), (4.05, 8.1, 8.1) + + cells_yz = new AlCell.move(4.05, 0.00, 0.00) [2].move(0.0, 8.10, 0.0 ) + [2].move(0.0, 0.0, 8.10) + + # The next command creates 12 AlCells (2x2x3) at: + # (0.0, 0.0, 0.0), (0.0, 0.0, 4.05), (0.0, 0.0, 8.1) + # (0.0, 8.1, 0.0), (0.0, 8.1, 4.05), (0.0, 8.1, 8.1) + # (8.1, 8.1, 0.0), (8.1, 8.1, 4.05), (8.1, 8.1, 8.1) + + cells_z = new AlCell [2].move(8.10, 0.00, 0.00) + [2].move(0.00, 8.10, 0.00) + [3].move(0.00, 0.00, 4.05) +} + + + +SierpinskiCubeLvl2 { + # Identical arrangement to SierpinskiCube1 (with 3x larger length scales) + cells_xz= new SierpinskiCubeLvl1.move(0.0,12.15,0.0) [2].move(24.3, 0.0, 0.0 ) + [2].move(0.0, 0.0, 24.3) + cells_yz= new SierpinskiCubeLvl1.move(12.15,0.0,0.0) [2].move(0.0, 24.3, 0.0 ) + [2].move(0.0, 0.0, 24.3) + cells_z = new SierpinskiCubeLvl1 [2].move(24.3, 0.00, 0.00) + [2].move(0.00, 24.3, 0.00) + [3].move(0.00, 0.00, 12.15) +} + + + +SierpinskiCubeLvl3 { + # Identical arrangement to SierpinskiCube2 (with 3x larger length scales) + cells_xz= new SierpinskiCubeLvl2.move(0.0,36.45,0.0) [2].move(72.9, 0.0, 0.0 ) + [2].move(0.0, 0.0, 72.9) + cells_yz= new SierpinskiCubeLvl2.move(36.45,0.0,0.0) [2].move(0.0, 72.9, 0.0 ) + [2].move(0.0, 0.0, 72.9) + cells_z = new SierpinskiCubeLvl2 [2].move(72.9, 0.00, 0.00) + [2].move(0.00, 72.9, 0.00) + [3].move(0.00, 0.00, 36.45) +} + diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/system.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/system.lt new file mode 100644 index 000000000..b226b77ee --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/system.lt @@ -0,0 +1,36 @@ +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 218.7 xlo xhi + 0.0 218.7 ylo yhi + 0.0 218.7 zlo zhi +} + +import "sierpinski_cubes.lt" + +cells_xyz = new SierpinskiCubeLvl3.move(0.0000, 0.0000, 0.0000) +cells_Xyz = new SierpinskiCubeLvl3.move(109.35, 0.0000, 0.0000) +cells_xYz = new SierpinskiCubeLvl3.move(0.0000, 109.35, 0.0000) +cells_xyZ = new SierpinskiCubeLvl3.move(0.0000, 0.0000, 109.35) + + + + + + + + + + + + + + + + +################################################################ +# The next command is not necessary: +# + create_var { $mol } # <-This forces all of the Al atoms in the crystal +# # to share the same molecule ID number. +# # Molecule ID numbers are not necessary. Ignore this. +# diff --git a/tools/moltemplate/examples/silly/sierpinski/run.in b/tools/moltemplate/examples/silly/sierpinski/run.in new file mode 100644 index 000000000..6b9ad17e6 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/run.in @@ -0,0 +1,38 @@ +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- +# +# Some of the run-settings below were stolen from: +# +# http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression + +# EQUILIBRATION +reset_timestep 0 +timestep 0.001 +velocity all create 300 12345 mom yes rot no +fix 1 all npt temp 300 300 1 iso 0 0 1 drag 1 + +# Output files +thermo 100 +thermo_style custom step ke pe press +dump dCoords all custom 100 traj.lammpstrj id type x y z ix iy iz + +run 20000 + +# Run for at least 10 picosecond (assuming 1 fs timestep) +run 10000 + + +###################################### +# SIMULATION DONE +print "All done" diff --git a/tools/moltemplate/moltemplate_manual.pdf b/tools/moltemplate/moltemplate_manual.pdf new file mode 100644 index 000000000..3297572cb Binary files /dev/null and b/tools/moltemplate/moltemplate_manual.pdf differ diff --git a/tools/moltemplate/src/bonds_by_type.py b/tools/moltemplate/src/bonds_by_type.py new file mode 100755 index 000000000..1c85eddc4 --- /dev/null +++ b/tools/moltemplate/src/bonds_by_type.py @@ -0,0 +1,379 @@ +#!/usr/bin/env python + +# Author: Andrew Jewett (jewett.aij at g mail) +# http://www.chem.ucsb.edu/~sheagroup +# License: 3-clause BSD License (See LICENSE.TXT) +# Copyright (c) 2011, Regents of the University of California +# All rights reserved. + +""" + bonds_by_type.py reads a LAMMPS data file (or an excerpt of a LAMMPS) + data file containing bonded many-body interactions by atom type + (and bond type), and generates a list of additional interactions + in LAMMPS format consistent with those type (to the standard out). + + Typical Usage: + + bonds_by_type.py -atoms atoms.data \\ + -bonds bonds.data \\ + -bondsbytype bonds_by_type.data \\ + > new_bonds.data + +""" + +# -bonds-ids-atom-pairs bonds_ids_atom_pairs.data \\ + +import sys +#from extract_lammps_data import * +#from nbody_by_type_lib import GenInteractions_str +import ttree_lex +#from ttree_lex import * +from lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid + + + +def LookupBondTypes(bond_types, + bond_ids, + bond_pairs, + lines_atoms, + lines_bonds, + lines_bondsbytype, + atom_style, + section_name, + prefix='', + suffix='', + bond_ids_offset=0): + #report_progress = False): + """ + LookupBondTypes() looks up bond types. + + Output: + ...It looks up the corresponding type of each bond and store it in the + "bond_types" list. (If the bond_ids were not specified by the user, + generate them and store them in the bond_ids list.) + + + Input (continued): + This function requires: + ...a list of bonded pairs of atoms + stored in the lines_bonds variable (from the "Data Bond List" + or "Data Bonds AtomId AtomId" sections) + ...and a list of atom types + stored in the lines_atoms variable (from the "Data Atoms" section) + ...and a list of bond-types-as-a-function-of-atom-types + stored in the lines_bondsbytype (from the "Data Bonds By Type" section) + + Generated bond_ids (if applicable) are of the form + prefix + str(number) + suffix + (where "number" begins at bond_ids_offset+1) + + """ + + column_names = AtomStyle2ColNames(atom_style) + i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) + + atomids = [] + atomtypes = [] + atomids2types = {} + + for iv in range(0, len(lines_atoms)): + line = lines_atoms[iv].strip() + if '#' in line: + icomment = line.find('#') + line = (line[:icomment]).strip() + if len(line) > 0: + tokens = ttree_lex.SplitQuotedString(line) + if ((len(tokens) <= i_atomid) or (len(tokens) <= i_atomtype)): + sys.stderr.write("\""+line+"\"\n") + raise(ttree_lex.InputError('Error not enough columns on line '+str(iv+1)+' of \"Atoms\" section.')) + tokens = ttree_lex.SplitQuotedString(line) + atomid = ttree_lex.EscCharStrToChar(tokens[i_atomid]) + atomids.append(atomid) + atomtype = ttree_lex.EscCharStrToChar(tokens[i_atomtype]) + atomtypes.append(atomtype) + atomids2types[atomid] = atomtype + + + assert(isinstance(bond_ids, list)) + assert(isinstance(bond_types, list)) + assert(isinstance(bond_pairs, list)) + del bond_ids[:] + del bond_types[:] + del bond_pairs[:] + + for ie in range(0, len(lines_bonds)): + + line = lines_bonds[ie].strip() + if '#' in line: + icomment = line.find('#') + line = (line[:icomment]).strip() + + if len(line) == 0: + continue + + tokens = ttree_lex.SplitQuotedString(line) + + if section_name == "Data Bonds AtomId AtomId": + if len(tokens) == 2: + bondid_n = bond_ids_offset + len(bond_ids) + 1 + bond_ids.append(prefix+str(bondid_n)+suffix) + bond_pairs.append( (ttree_lex.EscCharStrToChar(tokens[0]), + ttree_lex.EscCharStrToChar(tokens[1])) ) + else: + raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.')) + + elif section_name == "Data Bond List": + if len(tokens) == 3: + bond_ids.append(ttree_lex.EscCharStrToChar(tokens[0])) + bond_pairs.append( (ttree_lex.EscCharStrToChar(tokens[1]), + ttree_lex.EscCharStrToChar(tokens[2])) ) + else: + raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.')) + + #elif section_name == "Data Bonds BondType AtomId AtomId": + # if len(tokens) == 3: + # bondid_n = bond_ids_offset + len(bond_ids) + 1 + # bond_ids.append(prefix+str(bondid_n)+suffix) + # bond_types.append(ttree_lex.EscCharStrToChar(tokens[0])) + # bond_pairs.append( (ttree_lex.EscCharStrToChar(tokens[1]), + # ttree_lex.EscCharStrToChar(tokens[2])) ) + # else: + # raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.')) + + else: + raise(ttree_lex.InputError('Internal Error ('+g_program_name+'): Unknown section name: \"'+section_name+'\"')) + + + assert(len(bond_types) == 0) + typepattern_to_coefftypes = [] + + for i in range(0, len(lines_bondsbytype)): + line = lines_bondsbytype[i].strip() + if '#' in line: + icomment = line.find('#') + line = (line[:icomment]).strip() + if len(line) > 0: + tokens = ttree_lex.SplitQuotedString(line) + + if (len(tokens) != 3): + raise(ttree_lex.InputError('Error: Wrong number of columns in the \"Bonds By Type\" section of data file.\n' + 'Offending line:\n'+ + '\"'+line+'\"\n' + 'Expected 3 columns\n')) + + coefftype = ttree_lex.EscCharStrToChar(tokens[0]) + typepattern = [] + + for typestr in tokens[1:]: + if ((len(typestr) >= 2) and + (typestr[0] == '/') and (typestr[-1] == '/')): + regex_str = typestr[1:-1] + typepattern.append( re.compile(regex_str) ) + else: + typepattern.append(ttree_lex.EscCharStrToChar(typestr)) + + typepattern_to_coefftypes.append([typepattern, coefftype]) + + + + assert(len(bond_ids) == len(bond_pairs)) + + for ie in range(0,len(bond_ids)): + bond_types.append(None) + + for ie in range(0, len(bond_ids)): + bondid = bond_ids[ie] + (atomid1, atomid2) = bond_pairs[ie] + + #for n in range(0, len(typepattern_to_coefftypes)): + for typepattern, coefftype in typepattern_to_coefftypes: + + if atomid1 not in atomids2types: + raise ttree_lex.InputError('Error: atom \"'+atomid1+'\" not defined in \"Data Atoms\".\n' + ' This usually happens when the user mistypes one of the names of the\n' + ' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n' + ' To find out where the mistake occured, search the \n' + ' \"ttree_assignments.txt\" file for:\n' + ' \"'+atomid1+'\"\n') + + if atomid2 not in atomids2types: + raise ttree_lex.InputError('Error: atom \"'+atomid2+'\" not defined in \"Data Atoms\".\n' + ' This usually happens when the user mistypes one of the names of the\n' + ' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n' + ' To find out where the mistake occured, search the \n' + ' \"ttree_assignments.txt\" file for:\n' + ' \"'+atomid2+'\"\n') + + atomtype1 = atomids2types[atomid1] + atomtype2 = atomids2types[atomid2] + + # use string comparisons to check if atom types match the pattern + if (ttree_lex.MatchesAll((atomtype1, atomtype2), typepattern) or + ttree_lex.MatchesAll((atomtype2, atomtype1), typepattern)): + # ("MatchesAll()" defined in "ttree_lex.py") + + bond_types[ie] = coefftype + + for ie in range(0, len(bond_ids)): + if not bond_types[ie]: + atomtype1 = atomids2types[atomid1] + atomtype2 = atomids2types[atomid2] + raise ttree_lex.InputError('Error: No bond types defined for the bond between\n' + ' atoms '+atomid1+'(type '+atomtype1+') and '+atomid2+'(type '+atomtype2+')\n') + + + + +if __name__ == "__main__": + + g_program_name = __file__.split('/')[-1] # = 'nbody_by_type.py' + g_date_str = '2013-8-06' + g_version_str = '0.1' + + ####### Main Code Below: ####### + sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+' ') + if sys.version < '3': + sys.stderr.write(' (python version < 3)\n') + else: + sys.stderr.write('\n') + + try: + fname_atoms = None + fname_bonds = None + fname_bondsbytype = None + section_name = 'Data Bond List' # (This will be replaced later.) + atom_style = 'full' + prefix='' + suffix='' + bond_lack_types = False + + argv = [arg for arg in sys.argv] + + + # Loop over the remaining arguments not processed yet. + # These arguments are specific to the lttree.py program + # and are not understood by ttree.py: + i = 1 + while i < len(argv): + #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') + if ((argv[i].lower() == '-?') or + (argv[i].lower() == '--?') or + (argv[i].lower() == '-help') or + (argv[i].lower() == '-help')): + if i+1 >= len(argv): + sys.stdout.write(man_page_text+'\n') + sys.exit(0) + + elif argv[i].lower() == '-atoms': + if i+1 >= len(argv): + raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n' + ' text which might appear in the "Atoms" section of a LAMMPS data file.\n') + fname_atoms = argv[i+1] + del(argv[i:i+2]) + + elif argv[i].lower() == '-bonds': + if i+1 >= len(argv): + raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n' + ' text which might appear in the "Bonds" section of a LAMMPS data file.\n') + fname_bonds = argv[i+1] + del(argv[i:i+2]) + + elif argv[i].lower() == '-bond-list': + if i+1 >= len(argv): + raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name\n') + #raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n' + # ' text which might appear in the "Bonds No Types" section of a LAMMPS data file.\n') + fname_bonds = argv[i+1] + section_name = "Data Bond List" + del(argv[i:i+2]) + + elif argv[i].lower() == '-bondsbytype': + if i+1 >= len(argv): + raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name\n') + + #raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing\n' + # ' text which might appear in the "'+section_name+' By Type" section\n' + # ' of a LAMMPS data file.\n') + fname_bondsbytype = argv[i+1] + del(argv[i:i+2]) + + elif ((argv[i].lower() == '-atom-style') or + (argv[i].lower() == '-atom_style')): + if i+1 >= len(argv): + raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a an atom_style name.\n' + ' (Or single quoted string which includes a space-separated\n' + ' list of column names.)\n') + atom_style = argv[i+1] + del(argv[i:i+2]) + + elif argv[i].lower() == '-prefix': + if i+1 >= len(argv): + raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a prefix string\n' + ' (a string you want to appear to the left of the integer\n' + ' which counts the bonded interactions you have generated.)\n') + prefix = argv[i+1] + del(argv[i:i+2]) + + elif argv[i].lower() == '-suffix': + if i+1 >= len(argv): + raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a suffix string\n' + ' (a string you want to appear to the right of the integer\n' + ' which counts the bonded interactions you have generated.)\n') + prefix = argv[i+1] + del(argv[i:i+2]) + + elif argv[i][0] == '-': + raise ttree_lex.InputError('Error('+g_program_name+'):\n' + 'Unrecogized command line argument \"'+argv[i]+'\"\n') + else: + i += 1 + + if len(argv) != 1: + # if there are more than 2 remaining arguments, + problem_args = ['\"'+arg+'\"' for arg in argv[1:]] + raise ttree_lex.InputError('Syntax Error('+g_program_name+'):\n\n' + ' Problem with argument list.\n' + ' The remaining arguments are:\n\n' + ' '+(' '.join(problem_args))+'\n\n' + ' (The actual problem may be earlier in the argument list.)\n') + + bond_types = [] + bond_ids = [] + bond_pairs = [] + + fatoms = open(fname_atoms, 'r') + fbonds = open(fname_bonds, 'r') + fbondsbytype = open(fname_bondsbytype, 'r') + lines_atoms = fatoms.readlines() + lines_bonds = fbonds.readlines() + lines_bondsbytype = fbondsbytype.readlines() + fatoms.close() + fbonds.close() + fbondsbytype.close() + + LookupBondTypes(bond_types, + bond_ids, + bond_pairs, + lines_atoms, + lines_bonds, + lines_bondsbytype, + atom_style, + section_name, + prefix='', + suffix='') + + assert(len(bond_types) == len(bond_ids) == len(bond_pairs)) + + ie=0 + N = len(bond_types) + for ie in range(0, N): + sys.stdout.write(bond_ids[ie] + ' ' + + bond_types[ie] + ' ' + + bond_pairs[ie][0] + ' ' + + bond_pairs[ie][1] + '\n') + + + except (ValueError, ttree_lex.InputError) as err: + sys.stderr.write('\n'+str(err)+'\n') + sys.exit(-1) + diff --git a/tools/moltemplate/src/dump2data.py b/tools/moltemplate/src/dump2data.py new file mode 100755 index 000000000..604a69fa4 --- /dev/null +++ b/tools/moltemplate/src/dump2data.py @@ -0,0 +1,1262 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +""" +dump2data.py + +Extract dynamical degrees of freedom from a lammps DUMP file (from the stdin) +and construct a new DATA file (to the stdout). +A reference DATA file is needed (argument). + + basic usage +./dump2data.py orig_file.data < dump.lammpstrj > new_file.data + (This extract last frame, uses "full" atom_style.) + + options: +./dump2data.py [-t t -atomstyle style] orig.data < dump.lammpstrj > new.data + +""" + +# Authors: Andrew Jewett, Lieberman-Aiden group +# License: New BSD License +# Copyright (c) 2013 +# All rights reserved. + + +import sys +from collections import defaultdict +from operator import itemgetter, attrgetter + + +class InputError(Exception): + def __init__(self, err_msg): + self.err_msg = err_msg + def __str__(self): + return self.err_msg + + +def ErrorLeader(infile, lineno): + return '\"'+infile+'\", line '+str(lineno)+': ' + + +class MiscSettings(object): + def __init__(self): + self.tstart = None + self.tstop = None + self.timestep_str = '' + self.last_frame = False + self.center_frame = False + self.output_format = 'data' + self.input_format = 'dump' + self.multi = True + self.skip_interval = 1 + self.scale = None + + +class AtomStyleSettings(object): + def __init__(self): + # The following new member data indicate which columns store + # LAMMPS-specific information. + # The next 6 members store keep track of the different columns + # of the "Atoms" section of a LAMMPS data file: + self.column_names = [] #<--A list of column names (optional) + self.i_coords=[] #<--A triplet of integers indicating which columns store coordinate data + #self.ii_coords= [] #<--A list of triplets of column indexes storing coordinate data + self.ii_vects=[] #<--A list of triplets of column indexes storing directional data + # (such as dipole or ellipsoid orientations) + self.i_atomid=None #<--An integer indicating which column has the atomid + self.i_atomtype=None #<--An integer indicating which column has the atomtype + self.i_molid=None #<--An integer indicating which column has the molid, if applicable + + + +class DataSettings(AtomStyleSettings): + def __init__(self): + AtomStyleSettings.__init__(self) + self.contents = '' + self.file_name = '' + + + +# Atom Styles in LAMMPS as of 2011-7-29 +g_style_map = {'angle': ['atom-ID','molecule-ID','atom-type','x','y','z'], + 'atomic': ['atom-ID','atom-type','x','y','z'], + 'bond': ['atom-ID','molecule-ID','atom-type','x','y','z'], + 'charge': ['atom-ID','atom-type','q','x','y','z'], + 'colloid': ['atom-ID','atom-type','x','y','z'], + 'dipole': ['atom-ID','atom-type','q','x','y','z','mux','muy','muz'], + 'electron': ['atom-ID','atom-type','q','spin','eradius','x','y','z'], + 'ellipsoid':['atom-ID','atom-type','x','y','z','quatw','quati','quatj','quatk'], + 'full': ['atom-ID','molecule-ID','atom-type','q','x','y','z'], + 'granular': ['atom-ID','atom-type','diameter','density','x','y','z'], + 'molecular':['atom-ID','molecule-ID','atom-type','x','y','z'], + 'peri': ['atom-ID','atom-type','volume','density','x','y','z'], + 'hybrid': ['atom-ID','atom-type','x','y','z']} + + + + +def AtomStyle2ColNames(atom_style_string): + + atom_style_string = atom_style_string.strip() + if len(atom_style_string) == 0: + raise InputError('Error(dump2data): Invalid atom_style\n' + ' (The atom_style command was followed by an empty string.)\n') + atom_style_args = atom_style_string.split() + atom_style = atom_style_args[0] + + hybrid_args = atom_style_args[1:] + if (atom_style not in g_style_map): + if (len(atom_style_args) >= 2): + # If the atom_style_string includes at least 2 words, then we + # interpret this as a list of the individual column names + return atom_style_args + else: + raise InputError('Error(dump2data): Unrecognized atom_style: \"'+atom_style+'\"\n') + + if (atom_style != 'hybrid'): + return g_style_map[atom_style] + else: + column_names = ['atom-ID','atom-type','x','y','z'] + if (len(hybrid_args)==0): + raise InputError('Error(dump2data): atom_style hybrid must be followed by a sub_style.\n') + for sub_style in hybrid_args: + if (sub_style not in g_style_map): + raise InputError('Error(dump2data): Unrecognized atom_style: \"'+sub_style+'\"\n') + for cname in g_style_map[sub_style]: + if cname not in column_names: + column_names.append(cname) + + return column_names + + +def ColNames2AidAtypeMolid(column_names): + # Because of the diversity of ways that these + # numbers are referred to in the LAMMPS documentation, + # we have to be flexible and allow the user to refer + # to these quantities in a variety of ways. + # Hopefully this covers everything: + + i_atomid = None + if 'atom-ID' in column_names: + i_atomid = column_names.index('atom-ID') + elif 'atom−ID' in column_names: # (− is the character used in the manual) + i_atomid = column_names.index('atom−ID') + elif 'atomID' in column_names: + i_atomid = column_names.index('atomID') + elif 'atomid' in column_names: + i_atomid = column_names.index('atomid') + elif 'id' in column_names: + i_atomid = column_names.index('id') + elif 'atom' in column_names: + i_atomid = column_names.index('atom') + elif '$atom' in column_names: + i_atomid = column_names.index('$atom') + else: + raise InputError('Error(dump2data): List of column names lacks an \"atom-ID\"\n') + + i_atomtype = None + if 'atom-type' in column_names: + i_atomtype = column_names.index('atom-type') + elif 'atom−type' in column_names: # (− hyphen character used in manual) + i_atomtype = column_names.index('atom−type') + elif 'atomtype' in column_names: + i_atomtype = column_names.index('atomtype') + elif 'type' in column_names: + i_atomtype = column_names.index('type') + elif '@atom' in column_names: + i_atomtype = column_names.index('@atom') + else: + raise InputError('Error(dump2data): List of column names lacks an \"atom-type\"\n') + + i_molid = None + if 'molecule-ID' in column_names: + i_molid = column_names.index('molecule-ID') + elif 'molecule−ID' in column_names: # (− hyphen character used in manual) + i_molid = column_names.index('molecule−ID') + elif 'moleculeID' in column_names: + i_molid = column_names.index('moleculeID') + elif 'moleculeid' in column_names: + i_molid = column_names.index('moleculeid') + elif 'molecule' in column_names: + i_molid = column_names.index('molecule') + elif 'molID' in column_names: + i_molid = column_names.index('molID') + elif 'molid' in column_names: + i_molid = column_names.index('molid') + elif 'mol' in column_names: + i_molid = column_names.index('mol') + elif '$mol' in column_names: + i_molid = column_names.index('$mol') + else: + pass # some atom_types do not have a valid molecule-ID + + return i_atomid, i_atomtype, i_molid + + + +def ColNames2Coords(column_names): + """ Which of the columns correspond to coordinates + which must be transformed using rigid-body + (affine: rotation + translation) transformations? + This function outputs a list of lists of triplets of integers. + + """ + i_x = None + i_y = None + i_z = None + if 'x' in column_names: + i_x = column_names.index('x') + if 'y' in column_names: + i_y = column_names.index('y') + if 'z' in column_names: + i_z = column_names.index('z') + if (((i_x != None) != (i_y != None)) or + ((i_y != None) != (i_z != None)) or + ((i_z != None) != (i_x != None))): + raise InputError('Error(dump2data): columns must include \"x\", \"y\", and \"z\".\n') + return [[i_x, i_y, i_z]] + + +def ColNames2Vects(column_names): + """ Which of the columns correspond to coordinates + which must be transformed using rotations? + Some coordinates like dipole moments and + ellipsoid orientations should only be rotated + (not translated). + This function outputs a list of lists of triplets of integers. + + """ + vects = [] + i_mux = None + i_muy = None + i_muz = None + if 'mux' in column_names: + i_mux = column_names.index('mux') + if 'muy' in column_names: + i_muy = column_names.index('muy') + if 'muz' in column_names: + i_muz = column_names.index('muz') + if (((i_mux != None) != (i_muy != None)) or + ((i_muy != None) != (i_muz != None)) or + ((i_muz != None) != (i_mux != None))): + raise InputError('Error(dump2data): custom atom_style list must define mux, muy, and muz or none.\n') + if i_mux != None: + vects.append([i_mux, i_muy, i_muz]) + i_quati = None + i_quatj = None + i_quatk = None + if 'quati' in column_names: + i_quati = column_names.index('quati') + if 'quatj' in column_names: + i_quatj = column_names.index('quatj') + if 'quatk' in column_names: + i_quatk = column_names.index('quatk') + if (((i_quati != None) != (i_quatj != None)) or + ((i_quatj != None) != (i_quatk != None)) or + ((i_quatk != None) != (i_quati != None))): + raise InputError('Error(dump2data): custom atom_style list must define quati, quatj, and quatk or none.\n') + if i_quati != None: + vects.append([i_quati, i_quatj, i_quatk]) + return vects + + + + + +def ParseArgs(argv, + misc_settings, + data_settings, + warning_strings=None): + + # Loop over the remaining arguments not processed yet. + # These arguments are specific to the lttree.py program + # and are not understood by this program. + i = 1 + while i < len(argv): + #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') + if ((argv[i].lower() == '-atomstyle') or + (argv[i].lower() == '-atom_style') or + (argv[i].lower() == '-atom-style')): + in_init = [] + if i+1 >= len(argv): + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by a an atom_style name.\n' + ' (Or single quoted string which includes a space-separated\n' + ' list of column names.)\n') + data_settings.column_names = AtomStyle2ColNames(argv[i+1]) + sys.stderr.write(' \"Atoms\" column format:\n') + sys.stderr.write(' '+(' '.join(data_settings.column_names))+'\n') + + # ColNames2Coords() and ColNames2Vects() generate lists of + # triplets of integers, storing the column numbers containing + # x, y, and z coordinate values, and vx,vy,vz direction vectors. + data_settings.ii_vects = ColNames2Vects(data_settings.column_names) + ii_coords = ColNames2Coords(data_settings.column_names) + # This program assumes that there is only one coordinate triplet + # (x,y,z) for each atom. Hence we assume that len(ii_coords)==1 + assert(len(ii_coords) == 1) + data_settings.i_coords = ii_coords[0] + + # Now figure out which columns correspond to atomid, atomtype, molid + data_settings.i_atomid, data_settings.i_atomtype, data_settings.i_molid = ColNames2AidAtypeMolid(data_settings.column_names) + del(argv[i:i+2]) + + elif (argv[i].lower() == '-icoord'): + if i+1 >= len(argv): + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by list of integers\n' + ' corresponding to column numbers for coordinates in\n' + ' the \"Atoms\" section of a LAMMPS data file.\n') + ilist = argv[i+1].split() + if (len(ilist) % 3) != 0: + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by list of integers.\n' + ' This is usually a list of 3 intebers, but it can contain more.\n' + ' The number of cooridnate columns must be divisible by 3,\n' + ' (even if the simulation is in 2 dimensions)\n') + + #ii_coords = [] + #for i in range(0, len(ilist)/3): + # cols = [ilist[3*i]+1, ilist[3*i+1]+1, ilist[3*i+2]+1] + # ii_coords.append(cols) + #if ((len(ii_coords) != 0) or (len(ii_coords[0]) != 3)): + # raise InputError('Error(dump2data): Argument \"'+argv[i]+'\" must be followed by exactly 3 integers.\n') + + data_settings.i_coords = ilist + if (len(i_coords) != 3): + raise InputError('Error(dump2data): Argument \"'+argv[i]+'\" must be followed by exactly 3 integers.\n') + + data_settings.i_coords = ii_coords[0] + + del(argv[i:i+2]) + + elif (argv[i].lower() == '-ivect'): + if i+1 >= len(argv): + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by list of integers\n' + ' corresponding to column numbers for direction vectors in\n' + ' the \"Atoms\" section of a LAMMPS data file.\n') + ilist = argv[i+1].split() + if (len(ilist) % 3) != 0: + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by list of integers.\n' + ' This is usually a list of 3 intebers, but it can contain more.\n' + ' The number of cooridnate columns must be divisible by 3,\n' + ' (even if the simulation is in 2 dimensions)\n') + + data_settings.ii_vects = [] + for i in range(0, len(ilist)/3): + cols = [ilist[3*i]+1, ilist[3*i+1]+1, ilist[3*i+2]+1] + setting.ii_vects.append(cols) + # This should override any earlier settings as a result of the + # -atomstyle argument. So you can specify a custom list of column + # names using -atomstyle "list of column names", and then afterwards + # specify which of these columns correspond to direction vectors + # using the "-ivect" command line argument later on. + # This way, in theory you should be able to read columns from + # new custom atom-styles that have not been invented yet. + # (Although I haven't tested this.) + + del(argv[i:i+2]) + # i_atomid is not really needed for this program, but I load it anyway + elif ((argv[i].lower() == '-iatomid') or + (argv[i].lower() == '-iid') or + (argv[i].lower() == '-iatom-id')): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer\n' + ' (>=1) indicating which column in the \"Atoms\" section of a\n' + ' LAMMPS data file contains the atom id number (typically 1).\n' + ' (This argument is unnecessary if you use the -atomstyle argument.)\n') + i_atomid = int(argv[i+1])-1 + del(argv[i:i+2]) + # i_atomtype is not really needed for this program, but I load it anyway + elif ((argv[i].lower() == '-iatomtype') or + (argv[i].lower() == '-itype') or + (argv[i].lower() == '-iatom-type')): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer\n' + ' (>=1) indicating which column in the \"Atoms\" section of a\n' + ' LAMMPS data file contains the atom type.\n' + ' (This argument is unnecessary if you use the -atomstyle argument.)\n') + i_atomtype = int(argv[i+1])-1 + del(argv[i:i+2]) + # i_molid is not really needed for this program, but I load it anyway + elif ((argv[i].lower() == '-imolid') or + (argv[i].lower() == '-imol') or + (argv[i].lower() == '-imol-id') or + (argv[i].lower() == '-imoleculeid') or + (argv[i].lower() == '-imolecule-id')): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer\n' + ' (>=1) indicating which column in the \"Atoms\" section of a\n' + ' LAMMPS data file contains the molecule id number.\n' + ' (This argument is unnecessary if you use the -atomstyle argument.)\n') + del(argv[i:i+2]) + # Which frame do we want? + elif (argv[i].lower() == '-t'): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer indicating\n' + ' the frame you want to extract from the dump file (trajectory).\n' + ' This integer should match the timestep corresponding to the frame\n' + ' whose coordinates you wish to extract.\n') + misc_settings.timestep_str = argv[i+1] + del(argv[i:i+2]) + misc_settings.multi = False + misc_settings.last_frame = False + + elif (argv[i].lower() == '-tstart'): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer indicating\n' + ' the first frame you want to extract from the dump file (trajectory).\n' + ' This integer should match the timestep corresponding to the frame\n' + ' (after which) you wish to extract coordinates.\n') + misc_settings.tstart = float(argv[i+1]) + del(argv[i:i+2]) + misc_settings.multi = True + + elif (argv[i].lower() == '-tstop'): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an number indicating\n' + ' the first frame you want to extract from the dump file (trajectory).\n' + ' Frames after this timestep will be ignored.\n') + misc_settings.tstop = float(argv[i+1]) + del(argv[i:i+2]) + misc_settings.multi = True + + elif (argv[i].lower() == '-center'): + misc_settings.center_frame = True + del(argv[i:i+1]) + + elif ((argv[i].lower() == '-raw') or (argv[i].lower() == '-rawout')): + misc_settings.output_format = 'raw' + del(argv[i:i+1]) + + elif (argv[i].lower() == '-rawin'): + misc_settings.input_format = 'raw' + misc_settings.multi = False + del(argv[i:i+1]) + + elif ((argv[i].lower() == '-xyz') or (argv[i].lower() == '-xyzout')): + misc_settings.output_format = 'xyz' + del(argv[i:i+1]) + + elif (argv[i].lower() == '-xyzin'): + misc_settings.input_format = 'xyz' + misc_settings.multi = False + del(argv[i:i+1]) + + elif (argv[i].lower() == '-multi'): + misc_settings.multi = True + del(argv[i:i+1]) + + elif (argv[i].lower() == '-last'): + misc_settings.last_frame = True + misc_settings.multi = False + del(argv[i:i+1]) + + elif (argv[i].lower() == '-interval'): + misc_settings.skip_interval = int(argv[i+1]) + del(argv[i:i+2]) + + elif (argv[i].lower() == '-scale'): + misc_settings.scale = float(argv[i+1]) + del(argv[i:i+2]) + + elif ((argv[i][0] == '-') and (__name__ == "__main__")): + raise InputError('Error(dump2data): Unrecogized command line argument \"'+argv[i]+'\"\n') + else: + i += 1 + + usage_examples = \ +""" Typical usage: +dump2data.py orig_file.data < dump.lammpstrj > new_file.data + (This extracts last frame, uses "full" atom_style.) + Additional options: +dump2data.py -t t -atomstyle style orig.data < dump.lammpstrj > new.data +""" + + #if __name__ == "__main__": + + if (len(argv) > 2): + # if there are more than 2 remaining arguments, + # AND + # no other function will process the remaining argument list + # (ie. if __name__ == "__main__") + # THEN + raise InputError(' ----\n' + 'ERROR(dump2data): You have too many arguments (or unrecognized arguments):\n' + ' \"'+(' '.join(argv))+'\"\n' + ' ----\n' + +usage_examples) + elif (len(argv) < 2): + if misc_settings.output_format == 'data': + raise InputError(' ----\n' + 'ERROR(dump2data): Problem with argument list:\n' + ' Expected a LAMMPS .data file as an argument.\n' + ' ----\n' + +usage_examples) + else: + in_data_file = open(argv[1], 'r') + data_settings.file_name = argv[1]; + data_settings.contents = in_data_file.readlines() + in_data_file.close() + + #end of if-then statement for "if __name__ == "__main__"" + + if len(data_settings.i_coords) == 0: + if warning_strings != None: + warning_strings.append('WARNING(dump2data): atom_style unknown. (Use -atomstyle style. Assuming \"full\")') + warn_atom_style_unspecified = True + # The default atom_style is "full" + data_settings.column_names = AtomStyle2ColNames('full') + ii_coords = ColNames2Coords(data_settings.column_names) + # This program assumes that there is only one coordinate triplet + # (x,y,z) for each atom. Hence we assume that len(ii_coords)==1 + assert(len(ii_coords) == 1) + data_settings.i_coords = ii_coords[0] + data_settings.ii_vects = ColNames2Vects(data_settings.column_names) + data_settings.i_atomid, data_settings.i_atomtype, data_settings.i_molid = ColNames2AidAtypeMolid(data_settings.column_names) + + ### sys.stderr.write('########################################################\n' + ### '## WARNING: atom_style unspecified ##\n' + ### '## --> \"Atoms\" column data has an unknown format. ##\n' + ### '## Assuming atom_style = \"full\" ##\n' + ### '########################################################\n' + ### '## To specify the \"Atoms\" column format you can: ##\n' + ### '## 1) Use the -atom_style \"STYLE\" argument ##\n' + ### '## where \"STYLE\" is a string indicating a LAMMPS ##\n' + ### '## atom_style, including hybrid styles.(Standard ##\n' + ### '## atom styles defined in 2011 are supported.) ##\n' + ### '## 2) Use the -atom_style \"COL_LIST\" argument ##\n' + ### '## where \"COL_LIST" is a quoted list of strings ##\n' + ### '## indicating the name of each column. ##\n' + ### '## Names \"x\",\"y\",\"z\" are interpreted as ##\n' + ### '## atomic coordinates. \"mux\",\"muy\",\"muz\" ##\n' + ### '## and \"quati\",\"quatj\",\"quatk\" are ##\n' + ### '## interpreted as direction vectors. ##\n' + ### '## 3) Use the -icoord \"cx cy cz...\" argument ##\n' + ### '## where \"cx cy cz\" is a list of integers ##\n' + ### '## indicating the column numbers for the x,y,z ##\n' + ### '## coordinates of each atom. ##\n' + ### '## 4) Use the -ivect \"cmux cmuy cmuz...\" argument ##\n' + ### '## where \"cmux cmuy cmuz...\" is a list of ##\n' + ### '## integers indicating the column numbers for ##\n' + ### '## the vector that determines the direction of a ##\n' + ### '## dipole or ellipsoid (ie. a rotateable vector).##\n' + ### '## (More than one triplet can be specified. The ##\n' + ### '## number of entries must be divisible by 3.) ##\n' + ### '## 5) Include a ##\n' + ### '## write(\"in_init.txt\"){atom_style ...} ##\n' + ### '## statement in your .ttree file. ##\n' + ### '########################################################\n') + + + + +def GetIntAtomID(pair): + return int(pair[0]) + + + +def WriteFrameToData(out_file, + descr_str, + misc_settings, + data_settings, + natoms, + coords, + coords_ixiyiz, + vects, + velocities, + xlo_str, xhi_str, + ylo_str, yhi_str, + zlo_str, zhi_str, + xy_str, xz_str, yz_str): + + """ + Open a data file. Read the LAMMPS DATA file line by line. + When the line contains information which is also in the dump file, + replace that information with information from the dump file. + (Information from a dump file is stored in the arguments to this function.) + The resulting file also has LAMMPS DATA format. + + """ + + section = '' + firstline = True + for line in data_settings.contents: + line = line.strip() + ic = line.find('#') + if ic != -1: + line = line[:ic] + if firstline: # Construct a new descriptive header line: + if descr_str != None: + line = descr_str + firstline = False + + if (len(line) > 0): + # The initial section (section='') is assumed to be + # the "LAMMPS Description" section. This is where the + # box boundaries are specified. + if section == '': + tokens = line.split() + if ((len(tokens) >= 2) and + ((tokens[-2] == 'xlo') and (tokens[-1] == 'xhi')) and + ((xlo_str != None) and (xhi_str != None))): + tokens[0] = xlo_str + tokens[1] = xhi_str + line = ' '.join(tokens) + elif ((len(tokens) >= 2) and + ((tokens[-2] == 'ylo') and (tokens[-1] == 'yhi')) and + ((ylo_str != None) and (yhi_str != None))): + tokens[0] = ylo_str + tokens[1] = yhi_str + line = ' '.join(tokens) + elif ((len(tokens) >= 2) and + ((tokens[-2] == 'zlo') and (tokens[-1] == 'zhi')) and + ((zlo_str != None) and (zhi_str != None))): + tokens[0] = zlo_str + tokens[1] = zhi_str + line = ' '.join(tokens) + elif ((len(tokens) >= 3) and + ((tokens[-3] == 'xy') and + (tokens[-2] == 'xz') and + (tokens[-1] == 'yz')) and + ((xy_str != None) and + (xz_str != None) and + (yz_str != None))): + tokens[0] = xy_str + tokens[1] = xz_str + tokens[2] = yz_str + line = ' '.join(tokens) + if (line in set(['Masses', 'Velocities', 'Atoms', + 'Bond Coeffs', 'Angle Coeffs', + 'Dihedral Coeffs', 'Improper Coeffs', + 'Bonds', 'Angles', 'Dihedrals', 'Impropers'])): + section = line + else: + if (section == 'Atoms'): + tokens = line.split() + atomid = tokens[0] + if atomid in coords: + # Loop over all of the vector degrees of + # freedom of the particle, excluding coords + # (for example: mu_x, mu_y, mu_z, + # or quat_i, quat_j, quat_k) + # In principle, depending on the atom_style, + # there could be multiple vectors per atom. + for I in range(0,len(data_settings.ii_vects)): + vxvyvz = vects[atomid][I] + i_vx = data_settings.ii_vects[I][0] + i_vy = data_settings.ii_vects[I][1] + i_vz = data_settings.ii_vects[I][2] + if ((i_vx >= len(tokens)) or + (i_vy >= len(tokens)) or + (i_vz >= len(tokens))): + raise InputError('Error(dump2data): Atom style incompatible with data file.\n' + ' Specify the atom_style using -atomstyle style.\n') + if ((vxvyvz == None) or + (type(vxvyvz) is not tuple)): + assert(data_settings.column_names[i_vx] not in dump_column_names) + raise InputError('Error(dump2data): You have a vector coordinate in your DATA file named \"'+data_settings.column_names[i_vx]+'\"\n' + ' However there are no columns with this name in your DUMP file\n' + ' (or the column was not in the expected place).\n' + ' Hence, the atom styles in the dump and data files do not match.') + + # Replace the vector components with numbers + # from the dump file + tokens[i_vx] = vxvyvz[0] + tokens[i_vy] = vxvyvz[1] + tokens[i_vz] = vxvyvz[2] + + # Now loop over the coordinates of each atom. + #for I in range(0,len(data_settings.ii_coords)): + # xyz = coords[atomid][I] + # THIS LOOP IS SILLY. + # EACH ATOM ONLY HAS ONE SET OF X,Y,Z + # COORDINATES. COMMENTING OUT THIS LOOP: + # i_x = data_settings.ii_coords[I][0] + # i_y = data_settings.ii_coords[I][1] + # i_z = data_settings.ii_coords[I][2] + # USING THIS INSTEAD: + + xyz = coords[atomid] + i_x = data_settings.i_coords[0] + i_y = data_settings.i_coords[1] + i_z = data_settings.i_coords[2] + if ((i_x >= len(tokens)) or + (i_y >= len(tokens)) or + (i_z >= len(tokens))): + raise InputError('Error(dump2data): Atom style incompatible with data file.\n' + ' Specify the atom_style using -atomstyle style.\n') + # Replace the coordinates with coordinates from + # the dump file into tokens[i_x]... + tokens[i_x] = str(xyz[0]) + tokens[i_y] = str(xyz[1]) + tokens[i_z] = str(xyz[2]) + + # Are there there any integer coords + # (ix, iy, iz) in the dump file? + if coords_ixiyiz[atomid]: + assert(len(coords_ixiyiz[atomid]) == 3) + # Integer coords stored in the DATA file too? + if len(tokens)==(len(data_settings.column_names)+3): + # Then replace the last 3 columns of the + # line in the data file with: ix iy iz + tokens[-3] = coords_ixiyiz[atomid][0] + tokens[-2] = coords_ixiyiz[atomid][1] + tokens[-1] = coords_ixiyiz[atomid][2] + else: + if (not misc_settings.center_frame): + # Append them to the end of the line: + tokens.append(coords_ixiyiz[atomid][0]) + tokens.append(coords_ixiyiz[atomid][1]) + tokens.append(coords_ixiyiz[atomid][2]) + + # Now finally paste all the tokens together: + line = ' '.join(tokens) + + + elif (section == 'Velocities'): + tokens = line.split() + atomid = tokens[0] + if atomid in velocities: + + vxvyvz = velocities[atomid] + if len(tokens) < 4: + raise InputError('Error(dump2data): Not enough columns in the \"Velocities\" file.\n') + # Replace the coordinates with coordinates from + # the dump file into tokens[i_x]... + tokens[1] = str(vxvyvz[0]) + tokens[2] = str(vxvyvz[1]) + tokens[3] = str(vxvyvz[2]) + + # Now finally paste all the tokens together: + line = ' '.join(tokens) + + + out_file.write(line+'\n') + + + + + + + + + + + + + + + +if __name__ == "__main__": + + g_program_name = 'dump2data.py' + g_date_str = '2013-10-30' + g_version_str = 'v0.43' + + ####### Main Code Below: ####### + sys.stderr.write(g_program_name+' '+g_version_str+' '+g_date_str+' ') + #if sys.version < '3': + # sys.stderr.write(' (python version < 3)\n') + #else: + sys.stderr.write('\n') + + try: + data_settings = DataSettings() + misc_settings = MiscSettings() + warning_strings = [] + ParseArgs(sys.argv, + misc_settings, + data_settings, + warning_strings) + + # Open the lammps dump file (trajectory file) + # Skip to the line containing the correct frame/timestep. + # (this is the last frame by default). + # Read the "BOX BOUNDS" and the "ATOMS" sections. + # Store the x,y,z coordinates in the "coords" associative array + # (indexed by atom id, which could be non-numeric in general). + + section = '' + + #coords = defaultdict(list) + #coords_ixiyiz = defaultdict(list) + #vects = defaultdict(list) + #xlo_str = xhi_str = ylo_str = yhi_str = zlo_str = zhi_str = None + #xy_str = xz_str = yz_str = None + #natoms = -1 + #timestep_str = '' + + frame_coords = defaultdict(list) + frame_coords_ixiyiz = defaultdict(list) + frame_vects = defaultdict(list) + frame_velocities = defaultdict(list) + frame_xlo_str = frame_xhi_str = None + frame_ylo_str = frame_yhi_str = None + frame_zlo_str = frame_zhi_str = None + frame_xy_str = frame_xz_str = frame_yz_str = None + frame_natoms = -1 + frame_timestep_str = '' + i_atomid = i_atomtype = i_molid = -1 + i_x = i_y = i_z = i_xu = i_yu = i_zu = -1 + i_xs = i_ys = i_zs = i_xsu = i_ysu = i_zsu = -1 + + dump_column_names = [] + + #num_frames_in = -1 + num_frames_out = 0 + finished_reading_frame = False + read_last_frame = False + + #in_coord_file = open('traj_nvt.lammpstrj','r') + #in_coord_file = open('deleteme.lammpstrj','r') + in_coord_file = sys.stdin + + while True: + + line = in_coord_file.readline() + if line == '': # if EOF + if len(frame_coords) > 0: + finished_reading_frame = True + read_last_frame = True + + line = line.strip() + if (line.find('ITEM:') == 0): + section = line + if (section.find('ITEM: ATOMS ') == 0): + dump_column_names = line[12:].split() + i_atomid, i_atomtype, i_molid = \ + ColNames2AidAtypeMolid(dump_column_names) + #ii_coords = ColNames2Coords(dump_column_names) + + if 'x' in dump_column_names: + i_x = dump_column_names.index('x') + elif 'xu' in dump_column_names: + i_xu = dump_column_names.index('xu') + elif 'xs' in dump_column_names: + i_xs = dump_column_names.index('xs') + elif 'xsu' in dump_column_names: + i_xsu = dump_column_names.index('xsu') + else: + raise InputError('Error(dump2data): \"ATOMS\" section of dump file lacks a \"x\" column.\n'+ + ' (excerpt below)\n' + line) + + if 'y' in dump_column_names: + i_y = dump_column_names.index('y') + elif 'yu' in dump_column_names: + i_yu = dump_column_names.index('yu') + elif 'ys' in dump_column_names: + i_ys = dump_column_names.index('ys') + elif 'ysu' in dump_column_names: + i_ysu = dump_column_names.index('ysu') + else: + raise InputError('Error(dump2data): \"ATOMS\" section of dump file lacks a \"y\" column.\n'+ + ' (excerpt below)\n' + line) + + if 'z' in dump_column_names: + i_z = dump_column_names.index('z') + elif 'zu' in dump_column_names: + i_zu = dump_column_names.index('zu') + elif 'zs' in dump_column_names: + i_zs = dump_column_names.index('zs') + elif 'zsu' in dump_column_names: + i_zsu = dump_column_names.index('zsu') + else: + raise InputError('Error(dump2data): \"ATOMS\" section of dump file lacks a \"z\" column.\n'+ + ' (excerpt below)\n' + line) + + + + + + ii_vects = ColNames2Vects(dump_column_names) + if (len(ii_vects) != len(data_settings.ii_vects)): + raise InputError('Error(dump2data): atom styles in data and dump files differ.\n' + ' Some needed columns from the atom_styles are missing in the dump file.') + + i_ix = i_iy = i_iz = -1 + if 'ix' in dump_column_names: + i_ix = dump_column_names.index('ix') + if 'iy' in dump_column_names: + i_iy = dump_column_names.index('iy') + if 'iz' in dump_column_names: + i_iz = dump_column_names.index('iz') + + + i_vx = i_vy = i_vz = -1 + if 'vx' in dump_column_names: + i_vx = dump_column_names.index('vx') + if 'vy' in dump_column_names: + i_vy = dump_column_names.index('vy') + if 'vz' in dump_column_names: + i_vz = dump_column_names.index('vz') + + + elif (section.find('ITEM: BOX BOUNDS') == 0): + avec=[1.0, 0.0, 0.0] + bvec=[0.0, 1.0, 0.0] + cvec=[0.0, 0.0, 1.0] + + elif (section.find('ITEM: TIMESTEP') == 0): + if len(frame_coords) > 0: + finished_reading_frame = True + + elif ((len(line) > 0) and (line[0] != '#')): + if (section.find('ITEM: TIMESTEP') == 0): + finished_reading_frame = False + frame_timestep_str = line + frame_coords = defaultdict(list) + frame_coords_ixiyiz = defaultdict(list) + frame_vects = defaultdict(list) + frame_velocities = defaultdict(list) + frame_xlo_str = frame_xhi_str = None + frame_ylo_str = frame_yhi_str = None + frame_zlo_str = frame_zhi_str = None + frame_xy_str = frame_xz_str = frame_yz_str = None + + elif (section == 'ITEM: NUMBER OF ATOMS'): + frame_natoms = int(line) + + elif (section.find('ITEM: BOX BOUNDS') == 0): + is_triclinic = (section.find('xy xz yz') == 0) + + tokens = line.split() + if not frame_xlo_str: + assert(not frame_xhi_str) + frame_xlo_str = tokens[0] + frame_xhi_str = tokens[1] + avec[0] = float(frame_xhi_str) - float(frame_xlo_str) + if (is_triclinic and (len(tokens) > 2)): + frame_xy_str = tokens[2] + bvec[0] = float(frame_xy_str) + #See http://lammps.sandia.gov/doc/Section_howto.html#howto_12 + #sys.stderr.write('avec='+str(avec)+'\n') + + elif not frame_ylo_str: + assert(not frame_yhi_str) + frame_ylo_str = tokens[0] + frame_yhi_str = tokens[1] + bvec[1] = float(frame_yhi_str) - float(frame_ylo_str) + if (is_triclinic and (len(tokens) > 2)): + frame_xz_str = tokens[2] + cvec[0] = float(frame_xz_str) + #See http://lammps.sandia.gov/doc/Section_howto.html#howto_12 + #sys.stderr.write('bvec='+str(bvec)+'\n') + + elif not frame_zlo_str: + assert(not frame_zhi_str) + frame_zlo_str = tokens[0] + frame_zhi_str = tokens[1] + cvec = [0.0, 0.0, float(frame_zhi_str) - float(frame_zlo_str)] + if (is_triclinic and (len(tokens) > 2)): + frame_yz_str = tokens[2] + cvec[1] = float(frame_yz_str) + #See http://lammps.sandia.gov/doc/Section_howto.html#howto_12 + #sys.stderr.write('cvec='+str(cvec)+'\n') + + elif (section.find('ITEM: ATOMS') == 0): + tokens = line.split() + atomid = tokens[i_atomid] + + if ((i_x != -1) and (i_y != -1) and (i_z != -1)): + x = float(tokens[i_x]) #i_x determined above + y = float(tokens[i_y]) + z = float(tokens[i_z]) + + elif ((i_xu != -1) and (i_yu != -1) and (i_zu != -1)): + x = float(tokens[i_xu]) #i_x determined above + y = float(tokens[i_yu]) + z = float(tokens[i_zu]) + + elif ((i_xs != -1) and (i_ys != -1) and (i_zs != -1)): + xs = float(tokens[i_xs]) #i_xs determined above + ys = float(tokens[i_ys]) + zs = float(tokens[i_zs]) + + x = float(xlo_str) + xs*avec[0] + ys*bvec[0] + zs*cvec[0] + y = float(ylo_str) + xs*avec[1] + ys*bvec[1] + zs*cvec[1] + z = float(zlo_str) + xs*avec[2] + ys*bvec[2] + zs*cvec[2] + + # avec, bvec, cvec described here: + #http://lammps.sandia.gov/doc/Section_howto.html#howto_12 + + elif ((i_xsu != -1) and (i_ysu != -1) and (i_zsu != -1)): + xsu = float(tokens[i_xsu]) #i_xs determined above + ysu = float(tokens[i_ysu]) + zsu = float(tokens[i_zsu]) + + x = float(xlo_str) + xsu*avec[0] + ysu*bvec[0] + zsu*cvec[0] + y = float(ylo_str) + xsu*avec[1] + ysu*bvec[1] + zsu*cvec[1] + z = float(zlo_str) + xsu*avec[2] + ysu*bvec[2] + zsu*cvec[2] + + # Now deal with ix, iy, iz + if i_ix != -1: + ix = int(tokens[i_ix]) + if (misc_settings.center_frame or + (misc_settings.output_format != 'data')): + #sys.stderr.write('ix = '+str(ix)+', avec='+str(avec)+'\n') + x += ix*avec[0] + y += ix*avec[1] + z += ix*avec[2] + else: + if atomid not in frame_coords_ixiyiz: + frame_coords_ixiyiz[atomid] = ["0", "0", "0"] + else: + frame_coords_ixiyiz[atomid][0] = str(ix) + + if i_iy != -1: + iy = int(tokens[i_iy]) + if (misc_settings.center_frame or + (misc_settings.output_format != 'data')): + #sys.stderr.write('iy = '+str(iy)+', bvec='+str(bvec)+'\n') + x += iy*bvec[0] + y += iy*bvec[1] + z += iy*bvec[2] + else: + if atomid not in frame_coords_ixiyiz: + frame_coords_ixiyiz[atomid] = ["0", "0", "0"] + else: + frame_coords_ixiyiz[atomid][1] = str(iy) + + if i_iz != -1: + iz = int(tokens[i_iz]) + if (misc_settings.center_frame or + (misc_settings.output_format != 'data')): + #sys.stderr.write('iz = '+str(iz)+', cvec='+str(cvec)+'\n') + x += iz*cvec[0] + y += iz*cvec[1] + z += iz*cvec[2] + else: + if atomid not in frame_coords_ixiyiz: + frame_coords_ixiyiz[atomid] = ["0", "0", "0"] + else: + frame_coords_ixiyiz[atomid][2] = str(iz) + + #frame_coords[atomid] = [str(x), str(y), str(z)] + frame_coords[atomid] = [x, y, z] + + vx = 0.0 + vy = 0.0 + vz = 0.0 + if i_vx != -1: + vx = float(tokens[i_vx]) + if i_vy != -1: + vy = float(tokens[i_vy]) + if i_vz != -1: + vz = float(tokens[i_vz]) + + frame_velocities[atomid] = [vx, vy, vz] + + # Ugly detail: + # There can be multiple "vects" associated with each atom + # (for example, dipole moments, ellipsoid directions, etc..) + + if atomid not in frame_vects: + frame_vects[atomid] = [None for I in range(0,len(ii_vects))] + + for I in range(0, len(ii_vects)): + i_vx = ii_vects[I][0] + i_vy = ii_vects[I][1] + i_vz = ii_vects[I][2] + vx_str = tokens[i_vx] + vy_str = tokens[i_vy] + vz_str = tokens[i_vz] + + # Now the annoying part: + # Which vect is it (mux,muy,muz) or (quati,quatj,quatk)? + # The columns could be listed in a different order + # in the data file and in the dump file. + # Figure out which vector it is in the data file (stored + # in the integer "I_data") so that column names match. + name_vx = dump_column_names[i_vx] + name_vy = dump_column_names[i_vy] + name_vz = dump_column_names[i_vz] + i_vx_data = 0 + I_data = -1 + # This code is ugly and inneficient. + # I never want to touch this code again. (Hope it works) + while i_vx_data < len(data_settings.column_names): + if name_vx == data_settings.column_names[i_vx_data]: + I_data = 0 + while I_data < len(data_settings.ii_vects): + if ii_vects[I] == data_settings.ii_vects[I_data]: + break + I_data += 1 + + if (0= + # float(misc_settings.timestep_str)): + # num_frames_in = 1 + # if not misc_settings.multi: + # read_last_frame = True + # else: + # num_frames_in = 1 + + + + # Should we write out the coordinates in this frame? + write_this_frame = False + + if misc_settings.multi: + + write_this_frame = True + if (misc_settings.tstart and + (int(frame_timestep_str) < misc_settings.tstart)): + write_this_frame = False + if (misc_settings.tstop and + (int(frame_timestep_str) > misc_settings.tstop)): + write_this_frame = False + read_last_frame = True + + if misc_settings.tstart: + tstart = misc_settings.tstart + else: + tstart = 0 + + if ((int(frame_timestep_str) - tstart) + % + misc_settings.skip_interval) != 0: + write_this_frame = False + + else: + if misc_settings.last_frame: + if read_last_frame: + write_this_frame = True + else: + assert(misc_settings.timestep_str) + if (int(frame_timestep_str) >= + int(misc_settings.timestep_str)): + write_this_frame = True + read_last_frame = True + + + if write_this_frame: + + num_frames_out += 1 + + sys.stderr.write(' (writing frame '+str(num_frames_out)+ + ' at timestep '+frame_timestep_str+')\n') + + + # Print the frame + # First check which format to output the data: + if misc_settings.output_format == 'raw': + # Print out the coordinates in simple 3-column text format + for atomid, xyz in iter(sorted(frame_coords.items(), key=GetIntAtomID)): + if misc_settings.scale == None: + sys.stdout.write(str(xyz[0])+' '+str(xyz[1])+' '+str(xyz[2])+'\n') + else: + # Only convert to float and back if misc_settings.scale != None + sys.stdout.write(str(misc_settings.scale*float(xyz[0]))+' '+ + str(misc_settings.scale*float(xyz[1]))+' '+ + str(misc_settings.scale*float(xyz[2]))+'\n') + sys.stdout.write('\n') + + elif misc_settings.output_format == 'xyz': + # Print out the coordinates in simple 3-column text format + sys.stdout.write(str(len(frame_coords))+'\n') + descr_str = 'LAMMPS data from timestep '+frame_timestep_str + sys.stdout.write(descr_str+'\n') + for atomid, xyz in iter(sorted(frame_coords.items(), key=GetIntAtomID)): + if misc_settings.scale == None: + sys.stdout.write(str(atomid)+' '+ + str(xyz[0])+' '+ + str(xyz[1])+' '+ + str(xyz[2])+'\n') + else: + # Only convert to float and back if misc_settings.scale != None + sys.stdout.write(str(atomid)+' '+ + str(misc_settings.scale*float(xyz[0]))+' '+ + str(misc_settings.scale*float(xyz[1]))+' '+ + str(misc_settings.scale*float(xyz[2]))+'\n') + + else: + # Parse the DATA file specified by the user + # and replace appropriate lines or fields with + # the corresponding text from the DUMP file. + descr_str = 'LAMMPS data from timestep '+frame_timestep_str + if misc_settings.multi and (misc_settings.output_format == 'data'): + out_file_name = data_settings.file_name + '.'\ + + str(num_frames_out) + sys.stderr.write(' (creating file \"'+out_file_name+'\")\n') + out_file = open(out_file_name, 'w') + else: + out_file = sys.stdout + + WriteFrameToData(out_file, + descr_str, + misc_settings, + data_settings, + frame_natoms, + frame_coords, + frame_coords_ixiyiz, + frame_vects, + frame_velocities, + frame_xlo_str, frame_xhi_str, + frame_ylo_str, frame_yhi_str, + frame_zlo_str, frame_zhi_str, + frame_xy_str, frame_xz_str, frame_yz_str) + + #if misc_settings.multi: + # out_file.close() + + + #if num_frames_in >= 0: + # num_frames_in += 1 + + + if read_last_frame: + exit(0) + + + for warning_str in warning_strings: + sys.stderr.write(warning_str+'\n') + + + + except (ValueError, InputError) as err: + sys.stderr.write('\n'+str(err)+'\n') + sys.exit(-1) + diff --git a/tools/moltemplate/src/extract_lammps_data.py b/tools/moltemplate/src/extract_lammps_data.py new file mode 100755 index 000000000..4fe3ec743 --- /dev/null +++ b/tools/moltemplate/src/extract_lammps_data.py @@ -0,0 +1,119 @@ +#!/usr/bin/env python + +lammps_data_sections = set(['Atoms', + 'Masses', + 'Bonds', + 'Bond Coeffs', + 'Angles', + 'Angle Coeffs', + 'Dihedrals', + 'Dihedral Coeffs', + 'Impropers', + 'Improper Coeffs', + 'BondBond Coeffs', # class2 angles + 'BondAngle Coeffs', # class2 angles + 'MiddleBondTorsion Coeffs', # class2 dihedrals + 'EndBondTorsion Coeffs', # class2 dihedrals + 'AngleTorsion Coeffs', # class2 dihedrals + 'AngleAngleTorsion Coeffs', # class2 dihedrals + 'BondBond13 Coeffs', # class2 dihedrals + 'AngleAngle Coeffs', # class2 impropers + 'Angles By Type', # new. not standard LAMMPS + 'Dihedrals By Type',# new. not standard LAMMPS + 'Angles By Type']) # new. not standard LAMMPS + + +def DeleteComments(string, + escape='\\', + comment_char='#'): + escaped_state = False + for i in range(0,len(string)): + if string[i] in escape: + if escaped_state: + escaped_state = False + else: + escaped_state = True + elif string[i] == comment_char: + if not escaped_state: + return string[0:i] + return string + + + +def ExtractDataSection(f, + section_name, + comment_char = '#', + include_section_name = False, + return_line_nums = False): + + inside_section = False + if section_name in ('header','Header'): #"Header" section includes beginning + inside_section = True + + nonblank_encountered = False + nonheader_encountered = False + + i = 0 + for line_orig in f: + return_this_line = False + line = DeleteComments(line_orig).strip() + if line in lammps_data_sections: + nonheader_encountered = True + if section_name in ('header', 'Header'): + # The "header" section includes all lines at the beginning of the + # before any other section is encountered. + if nonheader_encountered: + return_this_line = False + else: + return_this_line = True + elif line == section_name: + inside_section = True + nonblank_encountered = False + if include_section_name: + return_this_line = True + # A block of blank lines (which dont immediately follow + # the section_name) signal the end of a section: + elif len(line) == 0: + if inside_section and include_section_name: + return_this_line = True + if nonblank_encountered: + inside_section = False + elif line[0] != comment_char: + if inside_section: + nonblank_encountered = True + return_this_line = True + + if return_this_line: + if return_line_nums: + yield i + else: + yield line_orig + + i += 1 + + + +if __name__ == "__main__": + + import sys + lines = sys.stdin.readlines() + exclude_sections = False + if sys.argv[1] == '-n': + exclude_sections = True + del sys.argv[1] + + if not exclude_sections: + for section_name in sys.argv[1:]: + for line in ExtractDataSection(lines, section_name): + sys.stdout.write(line) + else: + line_nums_exclude = set([]) + for section_name in sys.argv[1:]: + for line_num in ExtractDataSection(lines, + section_name, + include_section_name=True, + return_line_nums=True): + line_nums_exclude.add(line_num) + for i in range(0, len(lines)): + if i not in line_nums_exclude: + sys.stdout.write(lines[i]) diff --git a/tools/moltemplate/src/ltemplify.py b/tools/moltemplate/src/ltemplify.py new file mode 100755 index 000000000..a71af2598 --- /dev/null +++ b/tools/moltemplate/src/ltemplify.py @@ -0,0 +1,2236 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +# Author: Andrew Jewett (jewett.aij at g mail) +# http://www.chem.ucsb.edu/~sheagroup +# License: 3-clause BSD License (See LICENSE.TXT) +# Copyright (c) 2012, Regents of the University of California +# All rights reserved. + +""" +ltemplify.py + +The "ltemplify.py" script can be used to convert existing LAMMPS +input script and data files into a single .lt file +(which includes both topology and force-field information + for a single molecule in your system). + +Example: + + ltemplify.py -name Mol file.in file.data > mol.lt + +This creates a template for a new type of molecule (named "Mol"), +consisting of all the atoms in the lammps files you included, +and saves this data in a single ttree file ("mol.lt"). +This file can be used with moltemplate (ttree) to +define large systems containing this molecule. + +""" + +import sys +from ttree_lex import * +from lttree_styles import * + + + +def Intify(s): + if s.isdigit(): + return int(s) + elif s[0:2] == 'id': + return int(s[2:]) + elif s[0:4] == 'type': + return int(s[4:]) + else: + return s + +def StringToInterval(sel_str, slice_delim='*'): + i_slice = sel_str.find(slice_delim) + + if i_slice == -1: + if sel_str.isdigit(): + a = int(sel_str) + b = int(sel_str) + else: + a = sel_str + b = sel_str + + else: + a = sel_str[:i_slice] + b = sel_str[i_slice+len(slice_delim):] + + if (((len(a)>0) and (not a.isdigit())) or + ((len(b)>0) and (not b.isdigit()))): + raise InputError('Error: invalid selection string \"'+ + sel_str+'\"\n') + if (len(a) > 0): + a = int(a) + else: + a = None + + if (len(b) > 0): + b = int(b) + else: + b = None + + return a,b + + +# Selections are simply lists of 2-tuples (pairs) + +def LammpsSelectToIntervals(sel_str, slice_delim='*', or_delim=', '): + + """ + This function converts a string such as "1*4 6 9*12" into + a list of tuples, for example: [(1,4), (6,6), (9,12)] + In general, the of intervals has the form: + [(a1,b1), (a2,b2), (a3,b3), ... ] + + An atom is considered to belong to this selection + if it happens to lie within the closed interval [a,b] + for any pair of a,b values in the list of intervals. + If for a given pair a,b, either a or b is "None", then that a or b + value is not used to disqualify membership in the interval. + (Similar to -infinity or +infinity. In other words if a is set to None, + then to belong to the interval it is enough to be less than b.) + + """ + selection_list = [] + #tokens = sel_str.split(or_delim) <-- Not what we want when len(or_delim)>1 + tokens = LineLex.TextBlock2Lines(sel_str, or_delim, keep_delim=False) + for token in tokens: + token = token.strip() + (a,b) = StringToInterval(token, slice_delim) + selection_list.append((a, b)) + + return selection_list + + +def IntervalListToMinMax(interval_list): + min_a = None + max_b = None + for (a,b) in interval_list: + if ((not (type(a) is int)) or (not (type(b) is int))): + return None,None #only integer min/max makes sense. otherwise skip + + if (min_a == None) or (a < min_a): + min_a = a + if (max_b == None) or (b > max_b): + max_b = b + return min_a, max_b + + +def BelongsToSel(i, sel): + if (i == None) or (sel == None) or (len(sel) == 0): + # If the user has not specified a selection for this category, + # then by default all objects are accepted + return True + + elif (type(i) is str): + if i.isdigit(): + i = int(i) + else: + return True + + belongs = False + for interval in sel: + assert(len(interval) == 2) + if interval[0]: + if i >= interval[0]: + if (interval[1] == None) or (i <= interval[1]): + belongs = True + break + elif interval[1]: + if i <= interval[1]: + belongs = True + break + else: + # In that case, the user entered something like "*" + # which covers all possible numbers + belongs = True + break + + return belongs + + + +try: + + g_program_name = __file__.split('/')[-1] # = 'ltemplify.py' + g_version_str = '0.36' + g_date_str = '2013-8-22' + sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+'\n') + + non_empty_output = False + no_warnings = True + indent = 2 + cindent = 0 + atomid_selection = [] + atomtype_selection = [] + molid_selection = [] + mol_name = '' + + min_sel_atomid = None + min_sel_atomtype = None + min_sel_bondid = None + min_sel_bondtype = None + min_sel_angleid = None + min_sel_angletype = None + min_sel_dihedralid = None + min_sel_dihedraltype = None + min_sel_improperid = None + min_sel_impropertype = None + + max_sel_atomid = None + max_sel_atomtype = None + max_sel_bondid = None + max_sel_bondtype = None + max_sel_angleid = None + max_sel_angletype = None + max_sel_dihedralid = None + max_sel_dihedraltype = None + max_sel_improperid = None + max_sel_impropertype = None + + needed_atomids = set([]) + needed_atomtypes = set([]) + needed_bondids = set([]) + needed_bondtypes = set([]) + needed_angleids = set([]) + needed_angletypes = set([]) + needed_dihedralids = set([]) + needed_dihedraltypes = set([]) + needed_improperids = set([]) + needed_impropertypes = set([]) + + min_needed_atomtype = None + max_needed_atomtype = None + min_needed_bondtype = None + max_needed_bondtype = None + min_needed_angletype = None + max_needed_angletype = None + min_needed_dihedraltype = None + max_needed_dihedraltype = None + min_needed_impropertype = None + max_needed_impropertype = None + + + # To process the selections, we need to know the atom style: + atom_style_undefined = True + + i_atomid = None + i_atomtype = None + i_molid = None + + l_in_init = [] + l_in_settings = [] + l_in_masses = [] + l_in_pair_coeffs = [] + l_in_bond_coeffs = [] + l_in_angle_coeffs = [] + l_in_dihedral_coeffs = [] + l_in_improper_coeffs = [] + l_data_masses = [] + l_data_bond_coeffs = [] + l_data_angle_coeffs = [] + l_data_dihedral_coeffs = [] + l_data_improper_coeffs = [] + l_data_pair_coeffs = [] + l_data_atoms = [] + l_data_velocities = [] + l_data_bonds = [] + l_data_angles = [] + l_data_dihedrals = [] + l_data_impropers = [] + + # class2 force fields + l_data_bondbond_coeffs = [] + l_data_bondangle_coeffs = [] + l_data_middlebondtorsion_coeffs = [] + l_data_endbondtorsion_coeffs = [] + l_data_angletorsion_coeffs = [] + l_data_angleangletorsion_coeffs = [] + l_data_bondbond13_coeffs = [] + l_data_angleangle_coeffs = [] + + # non-point-like particles: + l_data_ellipsoids = [] + l_data_lines = [] + l_data_triangles = [] + + # automatic generation of bonded interactions by type: + l_data_angles_by_type = [] + l_data_dihedrals_by_type = [] + l_data_impropers_by_type = [] + + atoms_already_read = False + some_pair_coeffs_read = False + complained_atom_style_mismatch = False + infer_types_from_comments = False + + + argv = sys.argv + + i = 1 + + while i < len(argv): + + #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') + + if argv[i] == '-columns': + if i+1 >= len(argv): + raise InputError('Error: the \"'+argv[i]+'\" argument should be followed by a quoted\n' + ' string which contains a space-delimited list of the names of\n' + ' of columns in the \"Atoms\" section of the LAMMPS data file.\n' + ' If the list contains the symbols:\n' + ' \"atom-ID\" or \"atomid\", they are interpreted\n' + ' as unique atom ID numbers, and columns named\n' + ' \"atom-type\" or \"atomtype\" are interpreted\n' + ' as atom types. Finally, columns named\n' + ' \"molecule-ID\", \"molecule\", or \"mol-ID\", or \"mol\"\n' + ' are interpreted as unique molecule id numbers.\n' + 'Example:\n' + ' '+argv[i]+' \'atom-ID atom-type q polarizability molecule-ID x y z\'\n' + ' defines a custom atom_style containing the properties\n' + ' atom-ID atom-type q polarizability molecule-ID x y z\n' + ' Make sure you enclose the entire list in quotes.\n'); + column_names = argv[i+1].strip('\"\'').strip().split() + del(argv[i:i+2]) + + elif (argv[i] == '-ignore-comments'): + infer_types_from_comments = False + del(argv[i:i+1]) + + elif (argv[i] == '-infer-comments'): + infer_types_from_comments = True + del(argv[i:i+1]) + + elif ((argv[i] == '-name') or + (argv[i] == '-molname') or + (argv[i] == '-molecule-name') or + (argv[i] == '-molecule_name')): + if i+1 >= len(argv): + raise InputError('Error: '+argv[i]+' flag should be followed by a a molecule type name.\n') + cindent = 2 + indent += cindent + mol_name = argv[i+1] + del(argv[i:i+2]) + + elif ((argv[i].lower() == '-atomstyle') or + (argv[i].lower() == '-atom_style') or + (argv[i].lower() == '-atom-style')): + if i+1 >= len(argv): + raise InputError('Error: '+argv[i]+' flag should be followed by a an atom_style name.\n' + ' (or single quoted string which includes a space-separated\n' + ' list of column names).\n') + atom_style_undefined = False + column_names = AtomStyle2ColNames(argv[i+1]) + if (argv[i+1].strip().split()[0] in g_style_map): + l_in_init.append((' '*indent) + 'atom_style ' + argv[i+1] + '\n') + sys.stderr.write('\n \"Atoms\" column format:\n') + sys.stderr.write(' '+(' '.join(column_names))+'\n') + i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) + if i_molid: + sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+', i_molid='+str(i_molid+1)+')\n\n') + else: + sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+')\n') + del(argv[i:i+2]) + + elif ((argv[i].lower() == '-id') or + #(argv[i].lower() == '-a') or + #(argv[i].lower() == '-atoms') or + (argv[i].lower() == '-atomid') or + #(argv[i].lower() == '-atomids') or + (argv[i].lower() == '-atom-id') + #(argv[i].lower() == '-atom-ids') or + #(argv[i].lower() == '-$atom') or + #(argv[i].lower() == '-$atoms') + ): + if i+1 >= len(argv): + raise InputError('Error: '+argv[i]+' flag should be followed by a list of integers\n' + ' (or strings). These identify the group of atoms you want to\n' + ' to include in the template you are creating.\n') + atomid_selection += LammpsSelectToIntervals(argv[i+1]) + min_sel_atomid, max_sel_atomid = IntervalListToMinMax(atomid_selection) + del(argv[i:i+2]) + elif ((argv[i].lower() == '-type') or + #(argv[i].lower() == '-t') or + (argv[i].lower() == '-atomtype') or + (argv[i].lower() == '-atom-type') + #(argv[i].lower() == '-atomtypes') or + #(argv[i].lower() == '-atom-types') or + #(argv[i].lower() == '-@atom') or + #(argv[i].lower() == '-@atoms') or + #(argv[i].lower() == '-@atomtype') or + #(argv[i].lower() == '-@atomtypes') + ): + if i+1 >= len(argv): + raise InputError('Error: '+argv[i]+' flag should be followed by a list of integers.\n' + ' (or strings). These identify the group of atom types you want to\n' + ' to include in the template you are creating.\n') + atomtype_selection += LammpsSelectToIntervals(argv[i+1]) + min_sel_atomtype, max_sel_atomtype = IntervalListToMinMax(atomtype_selection) + del(argv[i:i+2]) + elif ((argv[i].lower() == '-mol') or + #(argv[i].lower() == '-m') or + (argv[i].lower() == '-molid') or + #(argv[i].lower() == '-molids') or + (argv[i].lower() == '-mol-id') or + #(argv[i].lower() == '-mol-ids') or + #(argv[i].lower() == '-molecule') or + (argv[i].lower() == '-moleculeid') or + (argv[i].lower() == '-molecule-id') + #(argv[i].lower() == '-molecules') or + #(argv[i].lower() == '-molecule-ids') or + #(argv[i].lower() == '-$mol') or + #(argv[i].lower() == '-$molecule') + ): + if i+1 >= len(argv): + sys.stderr.write('Error: '+argv[i]+' flag should be followed by a list of integers.\n' + ' (or strings). These identify the group of molecules you want to\n' + ' include in the template you are creating.\n') + molid_selection += LammpsSelectToIntervals(argv[i+1]) + del(argv[i:i+2]) + else: + i += 1 + + + # atom type names + atomtypes_name2int = {} + atomtypes_int2name = {} + #atomids_name2int = {} not needed + atomids_int2name = {} + atomids_by_type = {} + + + if atom_style_undefined: + # The default atom_style is "full" + column_names = AtomStyle2ColNames('full') + i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) + + #--------------------------------------------------------- + #-- The remaining arguments are files that the user wants + #-- us to read and convert. It is typical to have + #-- multiple input files, because LAMMPS users often + #-- store their force field parameters in either the LAMMPS + #-- data files and input script files, or both. + #-- We want to search all of the LAMMPS input files in + #-- order to make sure we extracted all the force field + #-- parameters (coeff commands). + #--------------------------------------------------------- + + for i_arg in range(1,len(argv)): + fname = argv[i_arg] + try: + lammps_file = open(fname, 'r') + except IOError: + raise InputError('Error: unrecognized argument (\"'+fname+'\"),\n' + ' OR unable to open file:\n' + '\n' + ' \"'+fname+'\"\n' + ' for reading.\n' + '\n' + ' (If you were not trying to open a file with this name,\n' + ' then there is a problem in your argument list.)\n') + + sys.stderr.write('reading file \"'+fname+'\"\n') + + atomid2type = {} + atomid2mol = {} + data_file_header_names = set(['LAMMPS Description', + 'Atoms', 'Masses', 'Velocities', 'Bonds', + 'Angles', 'Dihedrals', 'Impropers', + 'Pair Coeffs', + 'Bond Coeffs', 'Angle Coeffs', + 'Dihedral Coeffs', 'Improper Coeffs', + #class2 force fields: + 'BondBond Coeffs', 'BondAngle Coeffs', + 'MiddleBondTorsion Coeffs', 'EndBondTorsion Coeffs', + 'AngleTorsion Coeffs', 'AngleAngleTorsion Coeffs', + 'BondBond13 Coeffs', + 'AngleAngle Coeffs', + # non-point-like particles: + 'Ellipsoids', 'Triangles', 'Lines', + #specifying bonded interactions by type: + 'Angles By Type', 'Dihedrals By Type', 'Impropers By Type' + ]) + + lex=LineLex(lammps_file, fname) + lex.source_triggers = set(['include','import']) + # set up lex to accept most characters in file names: + lex.wordterminators = '(){}' + lex.whitespace + # set up lex to understand the "include" statement: + lex.source = 'include' + lex.escape = '\\' + + while lex: + infile = lex.infile + lineno = lex.lineno + line = lex.ReadLine() + if (lex.infile != infile): + infile = lex.infile + lineno = lex.lineno + + #sys.stderr.write(' processing \"'+line.strip()+'\", (\"'+infile+'\":'+str(lineno)+')\n') + + if line == '': + break + + tokens = line.strip().split() + if (len(tokens) > 0): + if ((tokens[0] == 'atom_style') and + atom_style_undefined): + + sys.stderr.write(' Atom Style found. Processing: \"'+line.strip()+'\"\n') + if atoms_already_read: + raise InputError('Error: The file containing the \"atom_style\" command must\n' + ' come before the data file in the argument list.\n' + ' (The templify program needs to know the atom style before reading\n' + ' the data file. Either change the order of arguments so that the\n' + ' LAMMPS input script file is processed before the data file, or use\n' + ' the \"-atom_style\" command line argument to specify the atom_style.)\n') + + column_names = AtomStyle2ColNames(line.split()[1]) + i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) + + sys.stderr.write('\n \"Atoms\" column format:\n') + sys.stderr.write(' '+(' '.join(column_names))+'\n') + if i_molid: + sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+', i_molid='+str(i_molid+1)+')\n\n') + else: + sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+')\n\n') + l_in_init.append((' '*indent)+line.lstrip()) + + elif (tokens[0] in set(['units', + 'angle_style', + 'bond_style', + 'dihedral_style', + 'impoper_style', + 'min_style', + 'pair_style', + 'pair_modify', + 'special_bonds', + 'kspace_style', + 'kspace_modify'])): + l_in_init.append((' '*indent)+line.lstrip()) + + #if (line.strip() == 'LAMMPS Description'): + # sys.stderr.write(' reading \"'+line.strip()+'\"\n') + # # skip over this section + # while lex: + # line = lex.ReadLine() + # if line.strip() in data_file_header_names: + # lex.push_raw_text(line) # <- Save line for later + # break + + elif (line.strip() == 'Atoms'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + atoms_already_read = True + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + if ((len(tokens) <= i_atomid) or + (len(tokens) <= i_atomtype) or + ((i_molid != None) and + (len(tokens) <= i_molid))): + raise InputError('Error: The number of columns in the \"Atoms\" section does\n' + ' not match the atom_style (see column name list above).\n') + elif ((len(tokens) != len(column_names)) and + (not complained_atom_style_mismatch)): + complained_atom_style_mismatch = True + sys.stderr.write('Warning: The number of columns in the \"Atoms\" section does\n' + ' not match the atom_style (see column name list above).\n') + # this is not a very serious warning. + #no_warnings = False <--no need. commenting out + + + atomid = Intify(tokens[i_atomid]) + atomtype = Intify(tokens[i_atomtype]) + + molid = None + if i_molid: + molid = Intify(tokens[i_molid]) + + atomid2type[atomid] = atomtype + if i_molid: + atomid2mol[atomid] = molid + + + if (BelongsToSel(atomid, atomid_selection) and + BelongsToSel(atomtype, atomtype_selection) and + BelongsToSel(molid, molid_selection)): + + tokens[i_atomid] = '$atom:id'+tokens[i_atomid] + #tokens[i_atomid] = '$atom:'+atomids_int2name[atomid] + # fill atomtype_int2str[] with a default name (change later): + #tokens[i_atomtype] = '@atom:type'+tokens[i_atomtype] + atomtype = int(tokens[i_atomtype]) + atomtype_name = 'type'+tokens[i_atomtype] + atomtypes_int2name[atomtype] = atomtype_name + tokens[i_atomtype] = '@atom:'+atomtype_name + + # I can't use atomids_int2names or atomtypes_int2names yet + # because they probably have not been defined yet. + # (Instead assign these names in a later pass.) + + if i_molid: + tokens[i_molid] = '$mol:id'+tokens[i_molid] + l_data_atoms.append((' '*indent)+(' '.join(tokens)+'\n')) + needed_atomids.add(atomid) + needed_atomtypes.add(int(atomtype)) + + for atomtype in needed_atomtypes: + if type(atomtype) is int: + if ((min_needed_atomtype == None) or + (min_needed_atomtype > atomtype)): + min_needed_atomtype = atomtype + if ((max_needed_atomtype == None) or + (max_needed_atomtype < atomtype)): + max_needed_atomtype = atomtype + + + elif (line.strip() == 'Masses'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + # Read the next line of text but don't skip comments + comment_char_backup = lex.commenters + lex.commenters = '' + line_orig = lex.ReadLine() + lex.commenters = comment_char_backup + + comment_text = '' + ic = line_orig.find('#') + line = line_orig[:ic] + if ic != -1: + comment_text = line_orig[ic+1:].strip() + + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + + tokens = line.strip().split() + if len(tokens) > 0: + atomtype = Intify(tokens[0]) + atomtype_name = str(atomtype) + + if comment_text != '': + comment_tokens = comment_text.split() + # Assume the first word after the # is the atom type name + atomtype_name = comment_tokens[0] + + if BelongsToSel(atomtype, atomtype_selection): + #tokens[0] = '@atom:type'+tokens[0] + l_data_masses.append((' '*indent)+(' '.join(tokens)+'\n')) + # infer atom type names from comment strings? + if infer_types_from_comments: + if atomtype_name in atomtypes_name2int: + raise InputError('Error: duplicate atom type names in mass section: \"'+atomtype_name+'\"\n' + ' (By default '+g_program_name+' attempts to infer atom type names from\n' + ' comments which appear in the \"Masses\" section of your data file.)\n' + ' You can avoid this error by adding the \"-ignore-comments\" argument.\n') + atomtypes_name2int[atomtype_name] = atomtype + atomtypes_int2name[atomtype] = atomtype_name + else: + atomtypes_int2name[atomtype] = 'type'+str(atomtype) + + + elif (line.strip() == 'Velocities'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + atomid = Intify(tokens[0]) + atomtype = None + if atomid in atomid2type: + atomtype = atomid2type[atomid] + moldid = None + if atomid in atomid2mol: + molid = atomid2mol[atomid] + if (BelongsToSel(atomid, atomid_selection) and + BelongsToSel(atomtype, atomtype_selection) and + BelongsToSel(molid, molid_selection)): + #tokens[0] = '$atom:id'+tokens[0] + tokens[0] = '$atom:'+atomids_int2name[atomid] + l_data_velocities.append((' '*indent)+(' '.join(tokens)+'\n')) + + # non-point-like-particles: + elif (line.strip() == 'Ellipsoids'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + atomid = Intify(tokens[0]) + atomtype = None + if atomid in atomid2type: + atomtype = atomid2type[atomid] + moldid = None + if atomid in atomid2mol: + molid = atomid2mol[atomid] + if (BelongsToSel(atomid, atomid_selection) and + BelongsToSel(atomtype, atomtype_selection) and + BelongsToSel(molid, molid_selection)): + #tokens[0] = '$atom:id'+tokens[0] + tokens[0] = '$atom:'+atomids_int2name[atomid] + l_data_ellipsoids.append((' '*indent)+(' '.join(tokens)+'\n')) + elif (line.strip() == 'Lines'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + atomid = Intify(tokens[0]) + atomtype = None + if atomid in atomid2type: + atomtype = atomid2type[atomid] + moldid = None + if atomid in atomid2mol: + molid = atomid2mol[atomid] + if (BelongsToSel(atomid, atomid_selection) and + BelongsToSel(atomtype, atomtype_selection) and + BelongsToSel(molid, molid_selection)): + #tokens[0] = '$atom:id'+tokens[0] + tokens[0] = '$atom:'+atomids_int2name[atomid] + l_data_lines.append((' '*indent)+(' '.join(tokens)+'\n')) + elif (line.strip() == 'Triangles'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + atomid = Intify(tokens[0]) + atomtype = None + if atomid in atomid2type: + atomtype = atomid2type[atomid] + moldid = None + if atomid in atomid2mol: + molid = atomid2mol[atomid] + if (BelongsToSel(atomid, atomid_selection) and + BelongsToSel(atomtype, atomtype_selection) and + BelongsToSel(molid, molid_selection)): + #tokens[0] = '$atom:id'+tokens[0] + tokens[0] = '$atom:'+atomids_int2name[atomid] + l_data_triangles.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Bonds'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + if (len(tokens) < 4): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical line in Bonds section:\n' + ' \"'+line.strip()+'\"\n') + #tokens[0] = '$bond:id'+tokens[0] + #tokens[1] = '@bond:type'+tokens[1] + atomids = [None, None] + atomtypes = [None, None] + molids = [None, None] + in_selections = True + some_in_selection = False + for n in range(0,2): + atomids[n] = Intify(tokens[2+n]) + if atomids[n] in atomid2type: + atomtypes[n] = atomid2type[atomids[n]] + if atomids[n] in atomid2mol: + molids[n] = atomid2mol[atomids[n]] + if (BelongsToSel(atomids[n], atomid_selection) and + BelongsToSel(atomtypes[n], atomtype_selection) and + BelongsToSel(molids[n], molid_selection)): + #tokens[2+n] = '$atom:id'+tokens[2+n] + #tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]] + some_in_selection = True + else: + in_selections = False + if in_selections: + l_data_bonds.append((' '*indent)+(' '.join(tokens)+'\n')) + elif some_in_selection: + sys.stderr.write('WARNING: SELECTION BREAKS BONDS\n') + sys.stderr.write(' (between atom ids: ') + + for n in range(0,2): + sys.stderr.write(str(atomids[n])+' ') + sys.stderr.write(')\n' + ' The atoms you selected are bonded\n' + ' to other atoms you didn\'t select.\n' + ' Are you sure you selected the correct atoms?\n') + no_warnings = False + + + + elif (line.strip() == 'Angles'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line == '': + break + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + if (len(tokens) < 5): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical line in Angles section:\n' + ' \"'+line.strip()+'\"\n') + #tokens[0] = '$angle:id'+tokens[0] + #tokens[1] = '@angle:type'+tokens[1] + atomids = [None, None, None] + atomtypes = [None, None, None] + molids = [None, None, None] + in_selections = True + some_in_selection = False + for n in range(0,3): + atomids[n] = Intify(tokens[2+n]) + if atomids[n] in atomid2type: + atomtypes[n] = atomid2type[atomids[n]] + if atomids[n] in atomid2mol: + molids[n] = atomid2mol[atomids[n]] + if (BelongsToSel(atomids[n], atomid_selection) and + BelongsToSel(atomtypes[n], atomtype_selection) and + BelongsToSel(molids[n], molid_selection)): + #tokens[2+n] = '$atom:id'+tokens[2+n] + #tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]] + some_in_selection = True + else: + in_selections = False + if in_selections: + l_data_angles.append((' '*indent)+(' '.join(tokens)+'\n')) + elif some_in_selection: + sys.stderr.write('WARNING: SELECTION BREAKS ANGLES\n') + sys.stderr.write(' (between atom ids: ') + for n in range(0,3): + sys.stderr.write(str(atomids[n])+' ') + sys.stderr.write(')\n' + ' The atoms you selected participate in 3-body \"Angle\"\n' + ' interactions with other atoms you didn\'t select.\n' + ' (They will be ignored.)\n' + ' Are you sure you selected the correct atoms?\n') + no_warnings = False + + + elif (line.strip() == 'Dihedrals'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + if (len(tokens) < 6): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical line in Dihedrals section:\n' + ' \"'+line.strip()+'\"\n') + #tokens[0] = '$dihedral:id'+tokens[0] + #tokens[1] = '@dihedral:type'+tokens[1] + atomids = [None, None, None, None] + atomtypes = [None, None, None, None] + molids = [None, None, None, None] + in_selections = True + some_in_selection = False + for n in range(0,4): + atomids[n] = Intify(tokens[2+n]) + if atomids[n] in atomid2type: + atomtypes[n] = atomid2type[atomids[n]] + if atomids[n] in atomid2mol: + molids[n] = atomid2mol[atomids[n]] + if (BelongsToSel(atomids[n], atomid_selection) and + BelongsToSel(atomtypes[n], atomtype_selection) and + BelongsToSel(molids[n], molid_selection)): + #tokens[2+n] = '$atom:id'+tokens[2+n] + #tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]] + some_in_selection = True + else: + in_selections = False + if in_selections: + l_data_dihedrals.append((' '*indent)+(' '.join(tokens)+'\n')) + elif some_in_selection: + sys.stderr.write('WARNING: SELECTION BREAKS DIHEDRALS\n') + sys.stderr.write(' (between atom ids: ') + for n in range(0,4): + sys.stderr.write(str(atomids[n])+' ') + sys.stderr.write(')\n' + ' The atoms you selected participate in 4-body \"Dihedral\"\n' + ' interactions with other atoms you didn\'t select.\n' + ' (They will be ignored.)\n' + ' Are you sure you selected the correct atoms?\n') + no_warnings = False + + + elif (line.strip() == 'Impropers'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + if (len(tokens) < 6): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical line in Impropers section:\n' + ' \"'+line.strip()+'\"\n') + #tokens[0] = '$improper:id'+tokens[0] + #tokens[1] = '@improper:type'+tokens[1] + atomids = [None, None, None, None] + atomtypes = [None, None, None, None] + molids = [None, None, None, None] + in_selections = True + some_in_selection = False + for n in range(0,4): + atomids[n] = Intify(tokens[2+n]) + if atomids[n] in atomid2type: + atomtypes[n] = atomid2type[atomids[n]] + if atomids[n] in atomid2mol: + molids[n] = atomid2mol[atomids[n]] + if (BelongsToSel(atomids[n], atomid_selection) and + BelongsToSel(atomtypes[n], atomtype_selection) and + BelongsToSel(molids[n], molid_selection)): + #tokens[2+n] = '$atom:id'+tokens[2+n] + #tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]] + some_in_selection = True + else: + in_selections = False + if in_selections: + l_data_impropers.append((' '*indent)+(' '.join(tokens)+'\n')) + elif some_in_selection: + sys.stderr.write('WARNING: SELECTION BREAKS IMPROPERS\n') + sys.stderr.write(' (between atom ids: ') + for n in range(0,4): + sys.stderr.write(str(atomids[n])+' ') + sys.stderr.write(')\n' + ' The atoms you selected participate in 4-body \"Improper\"\n' + ' interactions with other atoms you didn\'t select.\n' + ' (They will be ignored.)\n' + ' Are you sure you selected the correct atoms?\n') + no_warnings = False + + + elif (line.strip() == 'Bond Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + #tokens[0] = '@bond:type'+tokens[0] + l_data_bond_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Angle Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + #tokens[0] = '@angle:type'+tokens[0] + l_data_angle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Dihedral Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + #tokens[0] = '@dihedral:type'+tokens[0] + l_data_dihedral_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Improper Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + #tokens[0] = '@improper:type'+tokens[0] + l_data_improper_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Pair Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + some_pair_coeffs_read = True + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + if (len(tokens) < 2): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical line in Pair Coeffs section:\n' + ' \"'+line.strip()+'\"\n') + atomtype_i_str = tokens[0] + if '*' in atomtype_i_str: + raise InputError('PROBLEM near or before '+ErrorLeader(infile, lineno)+'\n' + ' As of 2012-7, moltemplate forbids use of the "\*\" wildcard\n' + ' character in the \"Pair Coeffs\" section.\n') + else: + i = int(atomtype_i_str) + if ((not i) or + BelongsToSel(i, atomtype_selection)): + i_str = '@atom:type'+str(i) + tokens[0] = i_str + l_data_pair_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (tokens[0] == 'pair_coeff'): + some_pair_coeffs_read = True + if (len(tokens) < 3): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical pair_coeff command:\n' + ' \"'+line.strip()+'\"\n') + l_in_pair_coeffs.append(' '*indent+line.strip()) + + elif (tokens[0] == 'mass'): + some_pair_coeffs_read = True + if (len(tokens) < 3): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical \"mass\" command:\n' + ' \"'+line.strip()+'\"\n') + l_in_masses.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (tokens[0] == 'bond_coeff'): + if (len(tokens) < 2): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical bond_coeff command:\n' + ' \"'+line.strip()+'\"\n') + #tokens[1] = '@bond:type'+tokens[1] + l_in_bond_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (tokens[0] == 'angle_coeff'): + if (len(tokens) < 2): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical angle_coeff command:\n' + ' \"'+line.strip()+'\"\n') + #tokens[1] = '@angle:type'+tokens[1] + l_in_angle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (tokens[0] == 'dihedral_coeff'): + if (len(tokens) < 2): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical dihedral_coeff command:\n' + ' \"'+line.strip()+'\"\n') + #tokens[1] = '@dihedral:type'+tokens[1] + l_in_dihedral_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + elif (tokens[0] == 'improper_coeff'): + if (len(tokens) < 2): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical improper_coeff command:\n' + ' \"'+line.strip()+'\"\n') + #tokens[1] = '@improper:type'+tokens[1] + l_in_improper_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + + # -- class2 force fields -- + elif (line.strip() == 'BondBond Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@angle:type'+tokens[0] + l_data_bondbond_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'BondAngle Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@angle:type'+tokens[0] + l_data_bondangle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'MiddleBondTorsion Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@dihedral:type'+tokens[0] + l_data_middlebondtorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'EndBondTorsion Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@dihedral:type'+tokens[0] + l_data_endbondtorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'AngleTorsion Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@dihedral:type'+tokens[0] + l_data_angletorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'AngleAngleTorsion Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@dihedral:type'+tokens[0] + l_data_angleangletorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'BondBond13 Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@dihedral:type'+tokens[0] + l_data_bondbond13_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'AngleAngle Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@improper:type'+tokens[0] + l_data_angleangle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Angles By Type'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@angle:type'+tokens[0] + l_data_angles_by_type.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Dihedrals By Type'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@dihedral:type'+tokens[0] + l_data_dihedrals_by_type.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Impropers By Type'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@improper:type'+tokens[0] + l_data_impropers_by_type.append((' '*indent)+(' '.join(tokens)+'\n')) + + else: + sys.stderr.write(' Ignoring line \"'+line.strip()+'\"\n') + + sys.stderr.write('\n\n') + + sys.stderr.write(' processing \"Atoms\" section (') + + # post-processing: + + if len(l_data_masses) == 0: + infer_types_from_comments = False + + # Pass 1 through l_data_atoms: + # Now do a second-pass throught the "l_data_atoms" section, and + # finish dealing with "infer_types_from_comments". + # During this pass, peplace the atomtype names and atomid names with + # atom type names which were inferred from comments read earlier. + + sys.stderr.write('pass1') + for i in range(0, len(l_data_atoms)): + tokens = l_data_atoms[i].split() + atomid = tokens[i_atomid] + if atomid.find('$atom:') == 0: + atomid = atomid[6:] + # convert to an integer + atomid = Intify(atomid) + + if infer_types_from_comments: + atomtype = tokens[i_atomtype] + # remove the "@atom:" prefix (we will put it back later) + if atomtype.find('@atom:') == 0: + atomtype = atomtype[6:] + # convert to an integer + atomtype = Intify(atomtype) + atomtype_name = atomtypes_int2name[atomtype] + if atomtype in atomids_by_type: + l_atomids = atomids_by_type[atomtype] + prev_count = len(l_atomids) + # lookup the most recently added atom of this type: + #prev_atomid_name = l_atomids[-1] + #ic = prev_atomid_name.rfind('_') + #prev_count = int(prev_atomid_name[ic+1:]) + atomid_name = atomtype_name+'_'+str(prev_count+1) + atomids_by_type[atomtype].append(atomid) + else: + atomids_by_type[atomtype] = [atomid] + atomid_name = atomtype_name+'_1' + atomids_int2name[atomid] = atomid_name + #atomids_name2str[atomid_name] = atomid + else: + atomids_int2name[atomid] = 'id'+str(atomid) + + sys.stderr.write(', pass2') + # Pass 2: If any atom types only appear once, simplify their atomid names. + for i in range(0, len(l_data_atoms)): + tokens = l_data_atoms[i].split() + + # remove the "@atom:" prefix (we will put it back later) + atomtype = tokens[i_atomtype] + if atomtype.find('@atom:') == 0: + atomtype = atomtype[6:] + atomtype = Intify(atomtype) + if infer_types_from_comments: + if len(atomids_by_type[atomtype]) == 1: + atomid = tokens[i_atomid] + if atomid.find('$atom:') == 0: + atomid = atomid[6:] + atomid = Intify(atomid) + atomtype_name = atomtypes_int2name[atomtype] + atomids_int2name[atomid] = atomtype_name + + sys.stderr.write(', pass3') + # Pass 3: substitute the atomid names and atom type names into l_data_atoms + for i in range(0, len(l_data_atoms)): + tokens = l_data_atoms[i].split() + atomid = tokens[i_atomid] + if atomid.find('$atom:') == 0: + atomid = atomid[6:] + # convert to an integer + atomid = Intify(atomid) + atomtype = tokens[i_atomtype] + if atomtype.find('@atom:') == 0: + atomtype = atomtype[6:] + atomtype = Intify(atomtype) + tokens = l_data_atoms[i].split() + tokens[i_atomid] = '$atom:'+atomids_int2name[atomid] + tokens[i_atomtype] = '@atom:'+atomtypes_int2name[atomtype] + l_data_atoms[i] = (' '*indent)+(' '.join(tokens)+'\n') + sys.stderr.write(')\n') + + + if len(l_data_atoms) == 0: + raise InputError('Error('+g_program_name+'): You have no atoms in you selection!\n' + '\n' + ' Either you have chosen a set of atoms, molecules, or atom types which\n' + ' does not exist, or there is a problem with (the format of) your\n' + ' arguments. Check the documentation and examples.\n') + + + # --- Now delete items that were not selected from the other lists --- + + # --- MASSES --- + + # delete masses for atom types we don't care about anymore: + i_line = 0 + while i_line < len(l_data_masses): + line = l_data_masses[i_line] + tokens = line.strip().split() + atomtype = Intify(tokens[0]) + if ((not (atomtype in needed_atomtypes)) and + (not ((len(atomtype_selection) > 0) and + BelongsToSel(atomtype, atomtype_selection)))): + del(l_data_masses[i_line]) + else: + atomtype_name = atomtypes_int2name[atomtype] + tokens[0] = '@atom:'+atomtype_name + l_data_masses[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + + + # --- PAIR COEFFS --- + + # delete data_pair_coeffs for atom types we don't care about anymore: + i_line = 0 + while i_line < len(l_data_pair_coeffs): + line = l_data_pair_coeffs[i_line] + tokens = line.strip().split() + assert(len(tokens) > 0) + split_colon = tokens[0].split(':') + assert(len(split_colon) == 2) + atomtype = Intify(split_colon[1]) + if ((not (atomtype in needed_atomtypes)) and + (not ((len(atomtype_selection) > 0) and + BelongsToSel(atomtype, atomtype_selection)))): + del(l_data_pair_coeffs[i_line]) + else: + i_line += 1 + + # delete in_pair_coeffs for atom we don't care about anymore: + i_line = 0 + while i_line < len(l_in_pair_coeffs): + line = l_in_pair_coeffs[i_line] + tokens = line.strip().split() + atomtype_i_str = tokens[1] + atomtype_j_str = tokens[2] + #if (('*' in atomtype_i_str) or + # ('*' in atomtype_j_str)): + # sys.stderr.write('WARNING: near or before '+ErrorLeader(infile, lineno)+'\n' + # ' pair_coeff command contains a \"*\" character.\n' + # ' Keep in mind that using moltemplate.sh you can manually change the\n' + # ' numbers assigned to each atom type (when using -a or -b). Make sure\n' + # ' nor to accidentally change the order of atom types in one of these\n' + # ' pair_coeff commands. For example, commands like\n' + # ' pair_coeff 10*4 20*10 0.15 3.6\n' + # ' can be generated by moltemplate.sh, however\n' + # ' they may be rejected by LAMMPS (because LAMMPS prefers this\n' + # ' pair_coeff 4*10 10*20 0.15 3.6)\n' + # ' Later on, you may want to check to make sure moltemplate.sh\n' + # ' is not doing this. (Fortunately you never have to worry unless\n' + # ' you are using the -a or -b arguments with moltemplate.sh)\n') + + if ('*' in atomtype_i_str): + atomtype_i_tokens = atomtype_i_str.split('*') + + if atomtype_i_tokens[0] == '': + if (min_sel_atomtype and + (min_sel_atomtype < min_needed_atomtype)): + i_a = min_sel_atomtype + else: + i_a = min_needed_atomtype + else: + i_a = Intify(atomtype_i_tokens[0]) + + if atomtype_i_tokens[1] == '': + if (max_sel_atomtype and + (max_sel_atomtype > max_needed_atomtype)): + i_b = max_sel_atomtype + else: + i_b = max_needed_atomtype + else: + i_b = Intify(atomtype_i_tokens[1]) + + else: + i_a = i_b = Intify(atomtype_i_str) + + i_a_final = None + i_b_final = None + for i in range(i_a, i_b+1): + if ((i in needed_atomtypes) or (min_sel_atomtype <= i)): + i_a_final = i + break + for i in reversed(range(i_a, i_b+1)): + if ((i in needed_atomtypes) or (max_sel_atomtype >= i)): + i_b_final = i + break + + #if i_a_final and i_b_final: + # if i_a_final == i_b_final: + # i_str = '@atom:type'+str(i_a_final) + # tokens[1] = i_str + # else: + # i_str = '@{atom:type'+str(i_a_final)+'}*@{atom:type'+str(i_b_final)+'}' + + + + if ('*' in atomtype_j_str): + atomtype_j_tokens = atomtype_j_str.split('*') + + if atomtype_j_tokens[0] == '': + if (min_sel_atomtype and + (min_sel_atomtype < min_needed_atomtype)): + j_a = min_sel_atomtype + else: + j_a = min_needed_atomtype + else: + j_a = Intify(atomtype_j_tokens[0]) + + if atomtype_j_tokens[1] == '': + if (max_sel_atomtype and + (max_sel_atomtype > max_needed_atomtype)): + j_b = max_sel_atomtype + else: + j_b = max_needed_atomtype + else: + j_b = Intify(atomtype_j_tokens[1]) + + else: + j_a = j_b = Intify(atomtype_j_str) + + j_a_final = None + j_b_final = None + for j in range(j_a, j_b+1): + if ((j in needed_atomtypes) or (min_sel_atomtype <= j)): + j_a_final = j + break + for j in reversed(range(j_a, j_b+1)): + if ((j in needed_atomtypes) or (max_sel_atomtype >= j)): + j_b_final = j + break + + #if j_a_final and j_b_final: + # if j_a_final == j_b_final: + # j_str = '@atom:type'+str(j_a_final) + # tokens[1] = j_str + # else: + # j_str = '@{atom:type'+str(j_a_final)+'}*@{atom:type'+str(j_b_final)+'}' + + + + if not (i_a_final and i_b_final and j_a_final and j_b_final): + del(l_in_pair_coeffs[i_line]) + elif (('*' in atomtype_i_str) or ('*' in atomtype_j_str)): + del(l_in_pair_coeffs[i_line]) + for i in range(i_a_final, i_b_final+1): + for j in range(j_a_final, j_b_final+1): + if j >= i: + #tokens[1] = '@atom:type'+str(i) + #tokens[2] = '@atom:type'+str(j) + tokens[1] = '@atom:'+atomtypes_int2name[i] + tokens[2] = '@atom:'+atomtypes_int2name[j] + l_in_pair_coeffs.insert(i_line, + (' '*indent)+(' '.join(tokens)+'\n')) + i_line += 1 + else: + #tokens[1] = '@atom:type'+tokens[1] + #tokens[2] = '@atom:type'+tokens[2] + tokens[1] = '@atom:'+atomtypes_int2name[int(tokens[1])] + tokens[2] = '@atom:'+atomtypes_int2name[int(tokens[2])] + l_in_pair_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + + + + # delete mass commands for atom types we don't care about anymore: + i_line = 0 + while i_line < len(l_in_masses): + line = l_in_masses[i_line] + tokens = line.strip().split() + atomtype_i_str = tokens[1] + #if (('*' in atomtype_i_str) or + # ('*' in atomtype_j_str)): + # sys.stderr.write('WARNING: near or before '+ErrorLeader(infile, lineno)+'\n' + # ' pair_coeff command contains a \"*\" character.\n' + # ' Keep in mind that using moltemplate.sh you can manually change the\n' + # ' numbers assigned to each atom type (when using -a or -b). Make sure\n' + # ' nor to accidentally change the order of atom types in one of these\n' + # ' pair_coeff commands. For example, commands like\n' + # ' pair_coeff 10*4 20*10 0.15 3.6\n' + # ' can be generated by moltemplate.sh, however\n' + # ' they may be rejected by LAMMPS (because LAMMPS prefers this\n' + # ' pair_coeff 4*10 10*20 0.15 3.6)\n' + # ' Later on, you may want to check to make sure moltemplate.sh\n' + # ' is not doing this. (Fortunately you never have to worry unless\n' + # ' you are using the -a or -b arguments with moltemplate.sh)\n') + + if ('*' in atomtype_i_str): + atomtype_i_tokens = atomtype_i_str.split('*') + + if atomtype_i_tokens[0] == '': + if (min_sel_atomtype and + (min_sel_atomtype < min_needed_atomtype)): + i_a = min_sel_atomtype + else: + i_a = min_needed_atomtype + else: + i_a = Intify(atomtype_i_tokens[0]) + + if atomtype_i_tokens[1] == '': + if (max_sel_atomtype and + (max_sel_atomtype > max_needed_atomtype)): + i_b = max_sel_atomtype + else: + i_b = max_needed_atomtype + else: + i_b = Intify(atomtype_i_tokens[1]) + + else: + i_a = i_b = Intify(atomtype_i_str) + + i_a_final = None + i_b_final = None + for i in range(i_a, i_b+1): + if ((i in needed_atomtypes) or (min_sel_atomtype <= i)): + i_a_final = i + break + for i in reversed(range(i_a, i_b+1)): + if ((i in needed_atomtypes) or (max_sel_atomtype >= i)): + i_b_final = i + break + #if i_a_final and i_b_final: + # if i_a_final == i_b_final: + # i_str = '@atom:type'+str(i_a_final) + # tokens[1] = i_str + # else: + # i_str = '@{atom:type'+str(i_a_final)+'}*@{atom:type'+str(i_b_final)+'}' + + if not (i_a_final and i_b_final and j_a_final and j_b_final): + del(l_in_masses[i_line]) + elif ('*' in atomtype_i_str): + del(l_in_masses[i_line]) + for i in range(i_a_final, i_b_final+1): + #tokens[1] = '@atom:type'+str(i) + tokens[1] = '@atom:'+atomtypes_int2name[i] + # CONTINUEHERE: CHECK THAT THIS IS WORKING + l_in_masses.insert(i_line, (' '*indent)+(' '.join(tokens)+'\n')) + i_line += 1 + else: + assert(i_a == i_b) + #tokens[1] = '@atom:type'+str(i_a) + tokens[1] = '@atom:'+atomtypes_int2name[i_a] + # CONTINUEHERE: CHECK THAT THIS IS WORKING + l_in_masses[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + + + + # --- BONDS AND BOND COEFFS --- + + # delete lines from data_bonds if they involve atoms we don't care about + i_line = 0 + while i_line < len(l_data_bonds): + line = l_data_bonds[i_line] + tokens = line.strip().split() + assert(len(tokens) == 4) + + bondid = Intify(tokens[0]) + bondtype = Intify(tokens[1]) + atomid1 = Intify(tokens[2]) + atomid2 = Intify(tokens[3]) + #if ((atomid1 in needed_atomids) and + # (atomid2 in needed_atomids)): + tokens[0] = '$bond:id'+str(bondid) + tokens[1] = '@bond:type'+str(bondtype) + #tokens[2] = '$atom:id'+str(atomid1) + #tokens[3] = '$atom:id'+str(atomid2) + tokens[2] = '$atom:'+atomids_int2name[atomid1] + tokens[3] = '$atom:'+atomids_int2name[atomid2] + needed_bondids.add(bondid) + needed_bondtypes.add(bondtype) + l_data_bonds[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + #else: + # del(l_data_bonds[i_line]) + + # delete data_bond_coeffs for bondtypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_bond_coeffs): + line = l_data_bond_coeffs[i_line] + tokens = line.strip().split() + bondtype = Intify(tokens[0]) + if (not (bondtype in needed_bondtypes)): + del(l_data_bond_coeffs[i_line]) + else: + tokens[0] = '@bond:type'+str(bondtype) + l_data_bond_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + # delete in_bond_coeffs for bondtypes we don't care about anymore: + for bondtype in needed_bondtypes: + if type(bondtype) is int: + if ((min_needed_bondtype == None) or + (min_needed_bondtype > bondtype)): + min_needed_bondtype = bondtype + if ((max_needed_bondtype == None) or + (max_needed_bondtype < bondtype)): + max_needed_bondtype = bondtype + i_line = 0 + while i_line < len(l_in_bond_coeffs): + line = l_in_bond_coeffs[i_line] + tokens = line.strip().split() + bondtype_str = tokens[1] + + if ('*' in bondtype_str): + bondtype_tokens = bondtype_str.split('*') + + if bondtype_tokens[0] == '': + i_a = min_needed_bondtype + else: + i_a = Intify(bondtype_tokens[0]) + + if bondtype_tokens[1] == '': + i_b = max_needed_bondtype + else: + i_b = Intify(bondtype_tokens[1]) + + else: + i_a = Intify(bondtype_str) + i_b = i_a + + if i_a < min_needed_bondtype: + i_a = min_needed_bondtype + if i_b > max_needed_bondtype: + i_b = max_needed_bondtype + + #if i_a == i_b: + # i_str = '@bond:type'+str(i_a) + # tokens[1] = i_str + #else: + # i_str = '@{bond:type'+str(j_a)+'}*@{bond:type'+str(j_b)+'}' + + if ('*' in bondtype_str): + del(l_in_bond_coeffs[i_line]) + for i in range(i_a, i_b+1): + if (i in needed_bondtypes): + tokens[1] = '@bond:type'+str(i) + l_in_bond_coeffs.insert(i_line, + (' '*indent)+(' '.join(tokens)+'\n')) + i_line += 1 + else: + if i_a < i_b: + raise InputError('Error: number of bond types in data file is not consistent with the\n' + ' number of bond types you have define bond_coeffs for.\n') + if (i_a == i_b) and (i_a in needed_bondtypes): + tokens[1] = '@bond:type'+str(i_a) + l_in_bond_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + else: + del(l_in_bond_coeffs[i_line]) + + + + + + # --- ANGLES AND ANGLE COEFFS --- + + # delete lines from data_angles if they involve atoms we don't care about + i_line = 0 + while i_line < len(l_data_angles): + line = l_data_angles[i_line] + tokens = line.strip().split() + assert(len(tokens) == 5) + + angleid = Intify(tokens[0]) + angletype = Intify(tokens[1]) + atomid1 = Intify(tokens[2]) + atomid2 = Intify(tokens[3]) + atomid3 = Intify(tokens[4]) + #if ((atomid1 in needed_atomids) and + # (atomid2 in needed_atomids)): + tokens[0] = '$angle:id'+str(angleid) + tokens[1] = '@angle:type'+str(angletype) + #tokens[2] = '$atom:id'+str(atomid1) + #tokens[3] = '$atom:id'+str(atomid2) + #tokens[4] = '$atom:id'+str(atomid3) + tokens[2] = '$atom:'+atomids_int2name[atomid1] + tokens[3] = '$atom:'+atomids_int2name[atomid2] + tokens[4] = '$atom:'+atomids_int2name[atomid3] + needed_angleids.add(angleid) + needed_angletypes.add(angletype) + l_data_angles[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + #else: + # del(l_data_angles[i_line]) + + # delete data_angle_coeffs for angletypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_angle_coeffs): + line = l_data_angle_coeffs[i_line] + tokens = line.strip().split() + angletype = Intify(tokens[0]) + if (not (angletype in needed_angletypes)): + del(l_data_angle_coeffs[i_line]) + else: + tokens[0] = '@angle:type'+str(angletype) + l_data_angle_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + # delete in_angle_coeffs for angletypes we don't care about anymore: + for angletype in needed_angletypes: + if type(angletype) is int: + if ((min_needed_angletype == None) or + (min_needed_angletype > angletype)): + min_needed_angletype = angletype + if ((max_needed_angletype == None) or + (max_needed_angletype < angletype)): + max_needed_angletype = angletype + i_line = 0 + while i_line < len(l_in_angle_coeffs): + line = l_in_angle_coeffs[i_line] + tokens = line.strip().split() + angletype_str = tokens[1] + + if ('*' in angletype_str): + angletype_tokens = angletype_str.split('*') + + if angletype_tokens[0] == '': + i_a = min_needed_angletype + else: + i_a = Intify(angletype_tokens[0]) + + if angletype_tokens[1] == '': + i_b = max_needed_angletype + else: + i_b = Intify(angletype_tokens[1]) + + else: + i_a = i_b = Intify(angletype_str) + + if i_a < min_needed_angletype: + i_a = min_needed_angletype + if i_b > max_needed_angletype: + i_b = max_needed_angletype + + #if i_a == i_b: + # i_str = '@angle:type'+str(i_a) + # tokens[1] = i_str + #else: + # i_str = '@{angle:type'+str(j_a)+'}*@{angle:type'+str(j_b)+'}' + + if ('*' in angletype_str): + del(l_in_angle_coeffs[i_line]) + for i in range(i_a, i_b+1): + if (i in needed_angletypes): + tokens[1] = '@angle:type'+str(i) + l_in_angle_coeffs.insert(i_line, + (' '*indent)+(' '.join(tokens)+'\n')) + i_line += 1 + else: + if i_a < i_b: + raise InputError('Error: number of angle types in data file is not consistent with the\n' + ' number of angle types you have define angle_coeffs for.\n') + if (i_a == i_b) and (i_a in needed_angletypes): + tokens[1] = '@angle:type'+str(i_a) + l_in_angle_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + else: + del(l_in_angle_coeffs[i_line]) + + + + # --- DIHEDRALS AND DIHEDRAL COEFFS --- + + # delete lines from data_dihedrals if they involve atoms we don't care about + i_line = 0 + while i_line < len(l_data_dihedrals): + line = l_data_dihedrals[i_line] + tokens = line.strip().split() + assert(len(tokens) == 6) + + dihedralid = Intify(tokens[0]) + dihedraltype = Intify(tokens[1]) + atomid1 = Intify(tokens[2]) + atomid2 = Intify(tokens[3]) + atomid3 = Intify(tokens[4]) + atomid4 = Intify(tokens[5]) + #if ((atomid1 in needed_atomids) and + # (atomid2 in needed_atomids)): + tokens[0] = '$dihedral:id'+str(dihedralid) + tokens[1] = '@dihedral:type'+str(dihedraltype) + #tokens[2] = '$atom:id'+str(atomid1) + #tokens[3] = '$atom:id'+str(atomid2) + #tokens[4] = '$atom:id'+str(atomid3) + #tokens[5] = '$atom:id'+str(atomid4) + tokens[2] = '$atom:'+atomids_int2name[atomid1] + tokens[3] = '$atom:'+atomids_int2name[atomid2] + tokens[4] = '$atom:'+atomids_int2name[atomid3] + tokens[5] = '$atom:'+atomids_int2name[atomid4] + + needed_dihedralids.add(dihedralid) + needed_dihedraltypes.add(dihedraltype) + l_data_dihedrals[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + #else: + # del(l_data_dihedrals[i_line]) + + # delete data_dihedral_coeffs for dihedraltypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_dihedral_coeffs): + line = l_data_dihedral_coeffs[i_line] + tokens = line.strip().split() + dihedraltype = Intify(tokens[0]) + if (not (dihedraltype in needed_dihedraltypes)): + del(l_data_dihedral_coeffs[i_line]) + else: + tokens[0] = '@dihedral:type'+str(dihedraltype) + l_data_dihedral_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + # delete in_dihedral_coeffs for dihedraltypes we don't care about anymore: + for dihedraltype in needed_dihedraltypes: + if type(dihedraltype) is int: + if ((min_needed_dihedraltype == None) or + (min_needed_dihedraltype > dihedraltype)): + min_needed_dihedraltype = dihedraltype + if ((max_needed_dihedraltype == None) or + (max_needed_dihedraltype < dihedraltype)): + max_needed_dihedraltype = dihedraltype + i_line = 0 + while i_line < len(l_in_dihedral_coeffs): + line = l_in_dihedral_coeffs[i_line] + tokens = line.strip().split() + dihedraltype_str = tokens[1] + + if ('*' in dihedraltype_str): + dihedraltype_tokens = dihedraltype_str.split('*') + + if dihedraltype_tokens[0] == '': + i_a = min_needed_dihedraltype + else: + i_a = Intify(dihedraltype_tokens[0]) + + if dihedraltype_tokens[1] == '': + i_b = max_needed_dihedraltype + else: + i_b = Intify(dihedraltype_tokens[1]) + + else: + i_a = i_b = Intify(dihedraltype_str) + + if i_a < min_needed_dihedraltype: + i_a = min_needed_dihedraltype + if i_b > max_needed_dihedraltype: + i_b = max_needed_dihedraltype + + #if i_a == i_b: + # i_str = '@dihedral:type'+str(i_a) + # tokens[1] = i_str + #else: + # i_str = '@{dihedral:type'+str(j_a)+'}*@{dihedral:type'+str(j_b)+'}' + + if ('*' in dihedraltype_str): + del(l_in_dihedral_coeffs[i_line]) + for i in range(i_a, i_b+1): + if (i in needed_dihedraltypes): + tokens[1] = '@dihedral:type'+str(i) + l_in_dihedral_coeffs.insert(i_line, + (' '*indent)+(' '.join(tokens)+'\n')) + i_line += 1 + else: + if i_a < i_b: + raise InputError('Error: number of dihedral types in data file is not consistent with the\n' + ' number of dihedral types you have define bond_coeffs for.\n') + if (i_a == i_b) and (i_a in needed_dihedraltypes): + tokens[1] = '@dihedral:type'+str(i_a) + l_in_dihedral_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + else: + del(l_in_dihedral_coeffs[i_line]) + + + + # --- IMPROPERS AND IMPROPER COEFFS --- + + # delete lines from data_impropers if they involve atoms we don't care about + i_line = 0 + while i_line < len(l_data_impropers): + line = l_data_impropers[i_line] + tokens = line.strip().split() + assert(len(tokens) == 6) + + improperid = Intify(tokens[0]) + impropertype = Intify(tokens[1]) + atomid1 = Intify(tokens[2]) + atomid2 = Intify(tokens[3]) + atomid3 = Intify(tokens[4]) + atomid4 = Intify(tokens[5]) + #if ((atomid1 in needed_atomids) and + # (atomid2 in needed_atomids)): + tokens[0] = '$improper:id'+str(improperid) + tokens[1] = '@improper:type'+str(impropertype) + #tokens[2] = '$atom:id'+str(atomid1) + #tokens[3] = '$atom:id'+str(atomid2) + #tokens[4] = '$atom:id'+str(atomid3) + #tokens[5] = '$atom:id'+str(atomid4) + tokens[2] = '$atom:'+atomids_int2name[atomid1] + tokens[3] = '$atom:'+atomids_int2name[atomid2] + tokens[4] = '$atom:'+atomids_int2name[atomid3] + tokens[5] = '$atom:'+atomids_int2name[atomid4] + + needed_improperids.add(improperid) + needed_impropertypes.add(impropertype) + l_data_impropers[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + #else: + # del(l_data_impropers[i_line]) + + # delete data_improper_coeffs for impropertypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_improper_coeffs): + line = l_data_improper_coeffs[i_line] + tokens = line.strip().split() + impropertype = Intify(tokens[0]) + if (not (impropertype in needed_impropertypes)): + del(l_data_improper_coeffs[i_line]) + else: + tokens[0] = '@improper:type'+str(impropertype) + l_data_improper_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + # delete in_improper_coeffs for impropertypes we don't care about anymore: + for impropertype in needed_impropertypes: + if type(impropertype) is int: + if ((min_needed_impropertype == None) or + (min_needed_impropertype > impropertype)): + min_needed_impropertype = impropertype + if ((max_needed_impropertype == None) or + (max_needed_impropertype < impropertype)): + max_needed_impropertype = impropertype + i_line = 0 + while i_line < len(l_in_improper_coeffs): + line = l_in_improper_coeffs[i_line] + tokens = line.strip().split() + impropertype_str = tokens[1] + + if ('*' in impropertype_str): + impropertype_tokens = impropertype_str.split('*') + + if impropertype_tokens[0] == '': + i_a = min_needed_impropertype + else: + i_a = Intify(impropertype_tokens[0]) + + if impropertype_tokens[1] == '': + i_b = max_needed_impropertype + else: + i_b = Intify(impropertype_tokens[1]) + + else: + i_a = i_b = Intify(impropertype_str) + + if i_a < min_needed_impropertype: + i_a = min_needed_impropertype + if i_b > max_needed_impropertype: + i_b = max_needed_impropertype + + #if i_a == i_b: + # i_str = '@improper:type'+str(i_a) + # tokens[1] = i_str + #else: + # i_str = '@{improper:type'+str(j_a)+'}*@{improper:type'+str(j_b)+'}' + + if ('*' in impropertype_str): + del(l_in_improper_coeffs[i_line]) + for i in range(i_a, i_b+1): + if (i in needed_impropertypes): + tokens[1] = '@improper:type'+str(i) + l_in_improper_coeffs.insert(i_line, + (' '*indent)+(' '.join(tokens)+'\n')) + i_line += 1 + else: + if i_a < i_b: + raise InputError('Error: number of improper types in data file is not consistent with the\n' + ' number of improper types you have define bond_coeffs for.\n') + if (i_a == i_b) and (i_a in needed_impropertypes): + tokens[1] = '@improper:type'+str(i_a) + l_in_improper_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + else: + del(l_in_improper_coeffs[i_line]) + + + + + + + + + if not some_pair_coeffs_read: + sys.stderr.write('Warning: No \"pair coeffs\" set.\n' + ' (No interactions between non-bonded atoms defined.)\n') + no_warnings = False + + #sys.stderr.write('Writing ttree data to standard out.\n' + # ' You can redirect this to a file using:\n'+ + # ' '+' '.join(sys.argv)+' > filename.ttree\n' + # ' ----------------------\n') + + if mol_name != '': + sys.stdout.write(mol_name + ' {\n') + + if len(l_in_init) > 0: + sys.stdout.write('\n### LAMMPS commands for initialization\n' + '### (These can be overridden later.)\n\n') + l_in_init.insert(0, (' '*cindent)+'write_once(\"'+in_init+'\") {\n') + l_in_init.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_init)) + if len(l_in_settings) > 0: + sys.stdout.write('\n### LAMMPS commands for settings\n' + '### (These can be overridden later.)\n\n') + l_in_settings.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_settings.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_settings)) + non_empty_output = True + if len(l_in_masses) > 0: + l_in_masses.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_masses.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_masses)) + non_empty_output = True + if len(l_in_pair_coeffs) > 0: + l_in_pair_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_pair_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_pair_coeffs)) + non_empty_output = True + if len(l_in_bond_coeffs) > 0: + l_in_bond_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_bond_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_bond_coeffs)) + non_empty_output = True + if len(l_in_angle_coeffs) > 0: + l_in_angle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_angle_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_angle_coeffs)) + non_empty_output = True + if len(l_in_dihedral_coeffs) > 0: + l_in_dihedral_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_dihedral_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_dihedral_coeffs)) + non_empty_output = True + if len(l_in_improper_coeffs) > 0: + l_in_improper_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_improper_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_improper_coeffs)) + non_empty_output = True + + if non_empty_output: + sys.stdout.write('\n### DATA sections\n\n') + + if len(l_data_masses) > 0: + l_data_masses.insert(0, (' '*cindent)+'write_once(\"'+data_masses+'\") {\n') + l_data_masses.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_masses)) + non_empty_output = True + if len(l_data_bond_coeffs) > 0: + l_data_bond_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bond_coeffs+'\") {\n') + l_data_bond_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_bond_coeffs)) + non_empty_output = True + if len(l_data_angle_coeffs) > 0: + l_data_angle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angle_coeffs+'\") {\n') + l_data_angle_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_angle_coeffs)) + non_empty_output = True + if len(l_data_dihedral_coeffs) > 0: + l_data_dihedral_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_dihedral_coeffs+'\") {\n') + l_data_dihedral_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_dihedral_coeffs)) + non_empty_output = True + if len(l_data_improper_coeffs) > 0: + l_data_improper_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_improper_coeffs+'\") {\n') + l_data_improper_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_improper_coeffs)) + non_empty_output = True + if len(l_data_pair_coeffs) > 0: + l_data_pair_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_pair_coeffs+'\") {\n') + l_data_pair_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_pair_coeffs)) + non_empty_output = True + + # class2 force fields: + if len(l_data_bondbond_coeffs) > 0: + l_data_bondbond_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bondbond_coeffs+'\") {\n') + l_data_bondbond_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_bondbond_coeffs)) + non_empty_output = True + if len(l_data_bondangle_coeffs) > 0: + l_data_bondangle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bondangle_coeffs+'\") {\n') + l_data_bondangle_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_bondangle_coeffs)) + non_empty_output = True + if len(l_data_middlebondtorsion_coeffs) > 0: + l_data_middlebondtorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_middlebondtorsion_coeffs+'\") {\n') + l_data_middlebondtorsion_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_middlebondtorsion_coeffs)) + non_empty_output = True + if len(l_data_endbondtorsion_coeffs) > 0: + l_data_endbondtorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_endbondtorsion_coeffs+'\") {\n') + l_data_endbondtorsion_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_endbondtorsion_coeffs)) + non_empty_output = True + if len(l_data_angletorsion_coeffs) > 0: + l_data_angletorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angletorsion_coeffs+'\") {\n') + l_data_angletorsion_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_angletorsion_coeffs)) + non_empty_output = True + if len(l_data_angleangletorsion_coeffs) > 0: + l_data_angleangletorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angleangletorsion_coeffs+'\") {\n') + l_data_angleangletorsion_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_angleangletorsion_coeffs)) + non_empty_output = True + if len(l_data_bondbond13_coeffs) > 0: + l_data_bondbond13_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bondbond13_coeffs+'\") {\n') + l_data_bondbond13_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_bondbond13_coeffs)) + non_empty_output = True + if len(l_data_angleangle_coeffs) > 0: + l_data_angleangle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angleangle_coeffs+'\") {\n') + l_data_angleangle_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_angleangle_coeffs)) + non_empty_output = True + + # automatic generation of bonded interactions by type: + if len(l_data_angles_by_type) > 0: + l_data_angles_by_type.insert(0, (' '*cindent)+'write_once(\"'+data_angles_by_type+'\") {\n') + l_data_angles_by_type.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_angles_by_type)) + non_empty_output = True + if len(l_data_dihedrals_by_type) > 0: + l_data_dihedrals_by_type.insert(0, (' '*cindent)+'write_once(\"'+data_dihedrals_by_type+'\") {\n') + l_data_dihedrals_by_type.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_dihedrals_by_type)) + non_empty_output = True + if len(l_data_impropers_by_type) > 0: + l_data_impropers_by_type.insert(0, (' '*cindent)+'write_once(\"'+data_impropers_by_type+'\") {\n') + l_data_impropers_by_type.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_impropers_by_type)) + non_empty_output = True + + if len(l_data_atoms) > 0: + l_data_atoms.insert(0, (' '*cindent)+'write(\"'+data_atoms+'\") {\n') + l_data_atoms.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_atoms)) + non_empty_output = True + else: + sys.stderr.write('Warning: missing \"Atoms\" section.\n' + ' (Did you include a LAMMPS data file in your argument list?)\n') + no_warnings = False + + # non-point-like particles + if len(l_data_ellipsoids) > 0: + l_data_ellipsoids.insert(0, (' '*cindent)+'write(\"'+data_ellipsoids+'\") {\n') + l_data_ellipsoids.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_ellipsoids)) + if len(l_data_lines) > 0: + l_data_lines.insert(0, (' '*cindent)+'write(\"'+data_lines+'\") {\n') + l_data_lines.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_lines)) + if len(l_data_triangles) > 0: + l_data_triangles.insert(0, (' '*cindent)+'write(\"'+data_triangles+'\") {\n') + l_data_triangles.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_triangles)) + + if len(l_data_velocities) > 0: + l_data_velocities.insert(0, (' '*cindent)+'write(\"'+data_velocities+'\") {\n') + l_data_velocities.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_velocities)) + if len(l_data_bonds) > 0: + l_data_bonds.insert(0, (' '*cindent)+'write(\"'+data_bonds+'\") {\n') + l_data_bonds.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_bonds)) + non_empty_output = True + if len(l_data_angles) > 0: + l_data_angles.insert(0, (' '*cindent)+'write(\"'+data_angles+'\") {\n') + l_data_angles.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_angles)) + non_empty_output = True + if len(l_data_dihedrals) > 0: + l_data_dihedrals.insert(0, (' '*cindent)+'write(\"'+data_dihedrals+'\") {\n') + l_data_dihedrals.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_dihedrals)) + non_empty_output = True + if len(l_data_impropers) > 0: + l_data_impropers.insert(0, (' '*cindent)+'write(\"'+data_impropers+'\") {\n') + l_data_impropers.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_impropers)) + non_empty_output = True + + if mol_name != '': + sys.stdout.write('\n} # end of \"'+mol_name+'\" type definition\n') + + #if non_empty_output and no_warnings: + if non_empty_output: + sys.stderr.write('\nWARNING: The '+g_program_name+' script has not been rigorously tested.\n' + ' Exotic (many-body) pair-styles and pair-styles with\n' + ' unusual syntax (such as hbond/dreiding) are not understood\n' + ' by '+g_program_name+' (...although they are supported by moltemplate).\n' + ' Please look over the resulting LT file and check for errors.\n' + ' Convert any remaining atom, bond, angle, dihedral, or improper id\n' + ' or type numbers to the corresponding $ or @-style counter variables.\n' + ' Feel free to report any bugs you find.\n' + ' (-Andrew Jewett 2013-8-14)\n') + +except (ValueError, InputError) as err: + sys.stderr.write('\n'+str(err)+'\n') + sys.exit(-1) diff --git a/tools/moltemplate/src/lttree.py b/tools/moltemplate/src/lttree.py new file mode 100755 index 000000000..5d1b34b7b --- /dev/null +++ b/tools/moltemplate/src/lttree.py @@ -0,0 +1,745 @@ +#!/usr/bin/env python + +# Author: Andrew Jewett (jewett.aij at g mail) +# http://www.chem.ucsb.edu/~sheagroup +# License: 3-clause BSD License (See LICENSE.TXT) +# Copyright (c) 2011, Regents of the University of California +# All rights reserved. + +""" +lttree.py + +lttree.py is an extension of the generic ttree.py program. +This version can understand and manipulate ttree-style templates which +are specialized for storing molecule-specific data for use in LAMMPS. + +The main difference between lttree.py and ttree.py is: +Unlike ttree.py, lttree.py understands rigid-body movement commands like +"rot()" and "move()" which allows it to reorient and move each copy +of a molecule to a new location. (ttree.py just ignores these commands. +Consequently LAMMPS input file (fragments) created with ttree.py have +invalid (overlapping) atomic coordinates and must be modified or aguemted +later (by loading atomic coordinates from a PDB file or an XYZ file). +lttree.py understands the "Data Atoms" section of a LAMMPS +data file (in addition to the various "atom_styles" which effect it). + +Additional LAMMPS-specific features may be added in the future. + +""" + +import sys +from ttree import * +from lttree_styles import * +from ttree_matrix_stack import * + +try: + unicode +except NameError: + # Python 3 + basestring = unicode = str + + + + +class LttreeSettings(BasicUISettings): + def __init__(self, + user_bindings_x=None, + user_bindings=None, + order_method='by_command'): + + BasicUISettings.__init__(self, + user_bindings_x, + user_bindings, + order_method) + + # The following new member data indicate which columns store + # LAMMPS-specific information. + # The next 6 members store keep track of the different columns + # of the "Data Atoms" section of a LAMMPS data file: + self.column_names = [] #<--A list of column names (optional) + self.ii_coords=[] #<--A list of triplets of column indexes storing coordinate data + self.ii_vects=[] #<--A list of triplets of column indexes storing directional data + # (such as dipole or ellipsoid orientations) + self.i_atomid=None #<--An integer indicating which column has the atomid + self.i_atomtype=None #<--An integer indicating which column has the atomtype + self.i_molid=None #<--An integer indicating which column has the molid, if applicable + self.infile=None # Name of the outermost file. This is the file + # which was read at the moment parsing begins. + + + + +def LttreeParseArgs(argv, settings): + + BasicUIParseArgs(argv, settings) + + # Loop over the remaining arguments not processed yet. + # These arguments are specific to the lttree.py program + # and are not understood by ttree.py: + i = 1 + while i < len(argv): + #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') + if ((argv[i].lower() == '-atomstyle') or + (argv[i].lower() == '-atom-style') or + (argv[i].lower() == '-atom_style')): + if i+1 >= len(argv): + raise InputError('Error('+g_program_name+'): The '+argv[i]+' flag should be followed by a LAMMPS\n' + ' atom_style name (or single quoted string containing a space-separated\n' + ' list of column names such as: atom-ID atom-type q x y z molecule-ID.)\n') + settings.column_names = AtomStyle2ColNames(argv[i+1]) + sys.stderr.write('\n \"'+data_atoms+'\" column format:\n') + sys.stderr.write(' '+(' '.join(settings.column_names))+'\n\n') + settings.ii_coords = ColNames2Coords(settings.column_names) + settings.ii_vects = ColNames2Vects(settings.column_names) + settings.i_atomid, settings.i_atomtype, settings.i_molid = ColNames2AidAtypeMolid(settings.column_names) + del(argv[i:i+2]) + elif (argv[i].lower() == '-icoord'): + if i+1 >= len(argv): + raise InputError('Error: '+argv[i]+' flag should be followed by list of integers\n' + ' corresponding to column numbers for coordinates in\n' + ' the \"'+data_atoms+'\" section of a LAMMPS data file.\n') + ilist = argv[i+1].split() + if (len(ilist) % 3) != 0: + raise InputError('Error: '+argv[i]+' flag should be followed by list of integers.\n' + ' This is usually a list of 3 integers, but it can contain more.\n' + ' The number of cooridnate columns must be divisible by 3,\n' + ' (even if the simulation is in 2 dimensions)\n') + settings.iaffinevects = [] + for i in range(0, len(ilist)/3): + cols = [int(ilist[3*i])+1, + int(ilist[3*i+1])+1, + int(ilist[3*i+2])+1] + settings.iaffinevects.append(cols) + del(argv[i:i+2]) + elif (argv[i].lower() == '-ivect'): + if i+1 >= len(argv): + raise InputError('Error: '+argv[i]+' flag should be followed by list of integers\n' + ' corresponding to column numbers for direction vectors in\n' + ' the \"'+data_atoms+'\" section of a LAMMPS data file.\n') + ilist = argv[i+1].split() + if (len(ilist) % 3) != 0: + raise InputError('Error: '+argv[i]+' flag should be followed by list of integers.\n' + ' This is usually a list of 3 integers, but it can contain more.\n' + ' The number of cooridnate columns must be divisible by 3,\n' + ' (even if the simulation is in 2 dimensions)\n') + settings.ivects = [] + for i in range(0, len(ilist)/3): + cols = [int(ilist[3*i])+1, + int(ilist[3*i+1])+1, + int(ilist[3*i+2])+1] + settings.ivects.append(cols) + del(argv[i:i+2]) + elif ((argv[i].lower() == '-iatomid') or + (argv[i].lower() == '-iid') or + (argv[i].lower() == '-iatom-id')): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error: '+argv[i]+' flag should be followed by an integer\n' + ' (>=1) indicating which column in the \"'+data_atoms+'\" section of a\n' + ' LAMMPS data file contains the atom id number (typically 1).\n' + ' (This argument is unnecessary if you use the -atomstyle argument.)\n') + i_atomid = int(argv[i+1])-1 + del(argv[i:i+2]) + elif ((argv[i].lower() == '-iatomtype') or + (argv[i].lower() == '-itype') or + (argv[i].lower() == '-iatom-type')): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error: '+argv[i]+' flag should be followed by an integer\n' + ' (>=1) indicating which column in the \"'+data_atoms+'\" section of a\n' + ' LAMMPS data file contains the atom type.\n' + ' (This argument is unnecessary if you use the -atomstyle argument.)\n') + i_atomtype = int(argv[i+1])-1 + del(argv[i:i+2]) + elif ((argv[i].lower() == '-imolid') or + (argv[i].lower() == '-imol') or + (argv[i].lower() == '-imol-id') or + (argv[i].lower() == '-imoleculeid') or + (argv[i].lower() == '-imolecule-id')): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error: '+argv[i]+' flag should be followed by an integer\n' + ' (>=1) indicating which column in the \"'+data_atoms+'\" section of a\n' + ' LAMMPS data file contains the molecule id number.\n' + ' (This argument is unnecessary if you use the -atomstyle argument.)\n') + i_molid = int(argv[i+1])-1 + del(argv[i:i+2]) + + elif ((argv[i][0] == '-') and (__name__ == "__main__")): + #elif (__name__ == "__main__"): + raise InputError('Error('+g_program_name+'):\n' + 'Unrecogized command line argument \"'+argv[i]+'\"\n') + else: + i += 1 + + + if __name__ == "__main__": + + # Instantiate the lexer we will be using. + # (The lexer's __init__() function requires an openned file. + # Assuming __name__ == "__main__", then the name of that file should + # be the last remaining (unprocessed) argument in the argument list. + # Otherwise, then name of that file will be determined later by the + # python script which imports this module, so we let them handle it.) + + if len(argv) == 1: + raise InputError('Error: This program requires at least one argument\n' + ' the name of a file containing ttree template commands\n') + elif len(argv) == 2: + try: + settings.lex = TemplateLexer(open(argv[1], 'r'), argv[1]) # Parse text from file + except IOError: + sys.stderr.write('Error: unable to open file\n' + ' \"'+argv[1]+'\"\n' + ' for reading.\n') + sys.exit(1) + del(argv[1:2]) + + else: + # if there are more than 2 remaining arguments, + problem_args = ['\"'+arg+'\"' for arg in argv[1:]] + raise InputError('Syntax Error('+g_program_name+'):\n\n' + ' Problem with argument list.\n' + ' The remaining arguments are:\n\n' + ' '+(' '.join(problem_args))+'\n\n' + ' (The actual problem may be earlier in the argument list.\n' + ' If these arguments are source files, then keep in mind\n' + ' that this program can not parse multiple source files.)\n' + ' Check the syntax of the entire argument list.\n') + + + + if len(settings.ii_coords) == 0: + sys.stderr.write('########################################################\n' + '## WARNING: atom_style unspecified ##\n' + '## --> \"'+data_atoms+'\" column data has an unknown format ##\n' + '## Assuming atom_style = \"full\" ##\n' + # '########################################################\n' + # '## To specify the \"'+data_atoms+'\" column format you can: ##\n' + # '## 1) Use the -atomstyle \"STYLE\" argument ##\n' + # '## where \"STYLE\" is a string indicating a LAMMPS ##\n' + # '## atom_style, including hybrid styles.(Standard ##\n' + # '## atom styles defined in 2011 are supported.) ##\n' + # '## 2) Use the -atomstyle \"COL_LIST\" argument ##\n' + # '## where \"COL_LIST" is a quoted list of strings ##\n' + # '## indicating the name of each column. ##\n' + # '## Names \"x\",\"y\",\"z\" are interpreted as ##\n' + # '## atomic coordinates. \"mux\",\"muy\",\"muz\" ##\n' + # '## are interpreted as direction vectors. ##\n' + # '## 3) Use the -icoord \"cx cy cz...\" argument ##\n' + # '## where \"cx cy cz\" is a list of integers ##\n' + # '## indicating the column numbers for the x,y,z ##\n' + # '## coordinates of each atom. ##\n' + # '## 4) Use the -ivect \"cmux cmuy cmuz...\" argument ##\n' + # '## where \"cmux cmuy cmuz...\" is a list of ##\n' + # '## integers indicating the column numbers for ##\n' + # '## the vector that determines the direction of a ##\n' + # '## dipole or ellipsoid (ie. a rotateable vector).##\n' + # '## (More than one triplet can be specified. The ##\n' + # '## number of entries must be divisible by 3.) ##\n' + '########################################################\n') + + # The default atom_style is "full" + settings.column_names = AtomStyle2ColNames('full') + settings.ii_coords = ColNames2Coords(settings.column_names) + settings.ii_vects = ColNames2Vects(settings.column_names) + settings.i_atomid, settings.i_atomtype, settings.i_molid = ColNames2AidAtypeMolid(settings.column_names) + + + + + + + + + +def TransformAtomText(text, matrix): + """ Apply transformations to the coordinates and other vector degrees + of freedom stored in the \"Data Atoms\" section of a LAMMPS data file. + This is the \"text\" argument. + The \"matrix\" stores the aggregate sum of combined transformations + to be applied. + + """ + + #sys.stderr.write('matrix_stack.M = \n'+ MatToStr(matrix) + '\n') + + lines = text.split('\n') + + for i in range(0, len(lines)): + line_orig = lines[i] + ic = line_orig.find('#') + if ic != -1: + line = line_orig[:ic] + comment = ' '+line_orig[ic:].rstrip('\n') + else: + line = line_orig.rstrip('\n') + comment = '' + + columns = line.split() + if len(columns) > 0: + if len(columns) == len(settings.column_names)+3: + raise InputError('Error: lttree.py does not yet support integer unit-cell counters \n' + ' within the \"'+data_atoms+'\" section of a LAMMPS data file.\n' + ' Instead please add the appropriate offsets (these offsets\n' + ' should be multiples of the cell size) to the atom coordinates\n' + ' in the data file, and eliminate the extra columns. Then try again.\n' + ' (If you get this message often, email me and I\'ll fix this limitation.)') + if len(columns) < len(settings.column_names): + raise InputError('Error: The number of columns in your data file does not\n' + ' match the LAMMPS atom_style you selected.\n' + ' Use the -atomstyle