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lammps/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/system.lt
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system.lt
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# 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
}
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