Homec4science
Diffusion lammps (master) Browse

lammps/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/system.lt
12150ffa7397master

Last Change
Raw File

system.lt
View Options

# LAMMPS supports a large number of force-field styles. We must select
# which ones we need. This information belongs in the "In Init" section (and
# (you can specify it anywhere in your LT files, multiple times if you like).
# If different molecules use different force-field styles, you can use hybrid
# styles. (In this example the molecules share the same pair_style.)
write_once("In Init") {
units real
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
pair_style lj/cut 9.0
# If you have charged molecules immersed in a salty implicit
# solvent, you might try something like this this instead:
# pair_style lj/cut/coul/debye 0.1 9.0
pair_modify mix arithmetic
dielectric 80.0
special_bonds lj 0.0 0.0 0.0
}
write_once("Data Boundary") {
0.0 36.0 xlo xhi
0.0 36.0 ylo yhi
-18.0 18.0 zlo zhi
}
import "solvent.lt"
import "walls.lt"
import "polymer.lt"
polymer = new Polymer
polymer.rot(-90.0, 0,0,1) # rotate it -90 degrees around the Y axis
polymer.move(19.5,22.5,16.5) # move it near the openning of the hole
####################### Notes: #########################
#
# In this example we deleted solvent and wall molecule objects.
# You can also delete a monomer inside the polymer. To do that use:
# delete polymer/monomers[6]
# You can also delete individual atoms, bonds, angles, dihedrals, & impropers
# from existing molecules. For example to delete an atom in the middle
# of the polymer try this. (Bonds and other interactions will also be removed.)
# delete polymer/monomers[6]/CA
# To delete a bond, try this
# delete polymer/bb6
# Note: This will not delete the angular interactions if they were explicitly
# defined (ie, using "Data Angles" instead of "Data Angles By Type").
# Delete explicit angle, dihedral, and improper interactions manually.
# Note: In both cases the two molecule fragments will keep the same mol counter.
c4science · Help