# Rhodopsin model

newton off
#package 	gpu force/neigh 2 2 1
#package 	gpu force 0 0 1

variable	x index 1
variable	y index 1
variable	z index 1

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 table 0
kspace_style    pppm 1e-4 

read_data       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

fix             2 all npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0 #mtk no pchain 0 tchain 1


special_bonds   charmm
 
thermo 10

thermo_style    custom step temp pe press pxx pyy pzz lx ly lz
timestep        1.0

run		100