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lammps/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/alkanes.lt
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alkanes.lt
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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
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