Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/tools/moltemplate/common/tip3p_1983.lt
4a1807d39739lammm-master-deprecated

Last Change
Raw File

tip3p_1983.lt
View Options

#############################################################
# 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
c4science · Help