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lammps/tools/moltemplate/common/same_files_with_comments/trappe1998_with_comments.lt
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trappe1998_with_comments.lt
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# This file contains force field parameters for the "TraPPE" potential used
# to model conformational change and interactions between coarse-grained
# alkane chains. This is a united-atom model. (Hydrogens are not represented
# explicitly.) This model is described in more detail here:
#
# Martin, M.G. and Siepmann. J.I.
# "Transferable potentials for phase equilibria. 1. united-atom description
# of n-alkanes." J. Phys. Chem. B, 102(14):2569–2577, 1998.
#
# ---- Force-Field File Format explanation ----
#
# Lammps-template files (LT files) contain object defintions like this:
#
# OBJECT_NAME {
# write commands { text and @ and $ variables...}
# }
#
# Often these objects are definitions of molecules
# which can be copied or pasted together to build larger molecules.
#
# However this file defines the static "TraPPE" object.
# "TraPPE" is not a molecule, but a collection of atom types,
# and a description of the interactions between them.
# These atoms can then be used inside other molecules.
# So you can think of the "TraPPE" object as an environment (namespace)
# describing the interactions between a limited set of atoms.
# Later on whenever you build a new molecule using TraPPE atoms,
# (for example using this syntax "@atom:.../TraPPE/CH2"),
# then the forces between them will be generated automatically.
#
# The dihedral (torsion) angle forces are given by
# U_dihedral(x) =
# = 0.5*(1.411036*(1+cos(x)) - 0.271016*(1-cos(2*x)) + 3.145034*(1+cos(3*x)))
# Note: The TraPPE authors suggest using bond-constraints like "SHAKE".
# Unfortunatley, in LAMMPS, SHAKE does not work for large molecules.
# Units:
# Energies in this file are in kCal/mole. (Where k_B = 0.001987207 in units of
# kCal mole^(-1) Kelvin^(-1), and 1 "thermochemical" calorie = 4.184000 Joule)
TraPPE {
write_once("Data Masses") {
@atom:CH2 14.1707
@atom:CH3 15.2507
@atom:CH4 16.3307
}
# The "atoms" named "CH2", "CH3", "CH4" denote carbon atoms
# bonded to 2, 3, and 4 hydrogen atoms, respectively.
# The following two "write_once()" statements instruct moltemplate.sh
# to automatically generate a 3-body "angle" or 4-body "dihedral"
# ineractions between any time 3 or 4 carbon atoms which are connected
# by consecutive "saturated". All three types of carbon atoms above
# have a name which matches "CH?". ('?' and '*' are wildcard characters.)
# Parameters for these "backbone" interactions are defined below.
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
}
# Force-field parameters:
write_once("In Settings") {
# -- Default settings/parameters for "TraPPE" --
# (Hybrid styles were used for portability.)
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
# (Interactions between different atom types in this list use mixing rules.)
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
}
# ------------------------------------------------------------------
# --------------- OPTIONAL DEFAULT SETTINGS BELOW -----------------
# ------------------------------------------------------------------
# -- All settings below are optional and can be overridden later. --
# -- They are only suggestions how to run LAMMPS with this model. --
# ------------------------------------------------------------------
# ------ lammps input script suggestions: ------
# Style suggestions:
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
}
# Here's an example of how define a LAMMPS group for all TraPPE atoms
# Note we have to list them all explicitly (CH2, CH3, CH4, not CH*).
# (Wildcards like '*' and '?' only work for "By Type" interactions, not here.)
write_once("In Settings") {
# -- Optional "TraPPE" groups --
group TraPPE type @atom:CH2 @atom:CH3 @atom:CH4
# (Atoms types between @{atom:CH2}-@{atom:CH4} belong to the "TraPPE" group.
# Note: All included atom types should explicitly appear in above list.)
}
} # class TraPPE
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