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lammps/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/monomer.lt
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monomer.lt
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# ----------------------------------------------------------------------
# -- 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).
# -------------------------------------------------------------------------
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