forked from lijiext/lammps
35 lines
697 B
Plaintext
35 lines
697 B
Plaintext
# Rhodopsin model
|
|
|
|
variable x index 1
|
|
variable y index 1
|
|
variable z index 1
|
|
variable t index 100
|
|
|
|
units real
|
|
neigh_modify delay 5 every 1
|
|
|
|
atom_style full
|
|
bond_style harmonic
|
|
angle_style charmm
|
|
dihedral_style charmm
|
|
improper_style harmonic
|
|
pair_style lj/charmm/coul/long 8.0 10.0
|
|
pair_modify mix arithmetic
|
|
kspace_style pppm 1e-4
|
|
|
|
read_data ../../bench/data.rhodo
|
|
|
|
replicate $x $y $z
|
|
|
|
fix 1 all shake 0.0001 5 0 m 1.0 a 232
|
|
fix 2 all npt temp 300.0 300.0 100.0 &
|
|
z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
|
|
|
|
special_bonds charmm
|
|
|
|
thermo 100
|
|
thermo_style multi
|
|
timestep 2.0
|
|
|
|
run $t
|