# Created by charmm2lammps v1.9.1 on Mon 13 Dec 2021 12:44:15 AM +0330
# Command: charmm2lammps.pl all27_prot_lipid water1_autopsf

echo            both
units           real
boundary        p p p
neigh_modify    delay 2 every 1
timestep        1
atom_style      full

bond_style      harmonic
angle_style     harmonic


read_data       solvate.data

	
bond_coeff 1 469.0  1.0     #H-O
bond_coeff 2 450.0  1.418      #C-C


angle_coeff 1  85.0  109.47    #H-O-H


set  type 1 charge 0.4238
set  type 2 charge -0.8476




pair_style       lj/charmm/coul/long 8.0 10.0 
pair_coeff     1  1     0.0     0.0     #H-H
pair_coeff     2  2    0.1553    3.166     #O-O
pair_coeff     3  3     0.07    3.9848     #C-C

pair_coeff     1  2    0.0     0.0     #H-O
pair_coeff     1  3      0.0     1.9924     #H-C
pair_coeff     2  3      0.104264     3.5754     #O-C

pair_modify     mix arithmetic
kspace_style    pppm 1e-6
#kspace_style pppm/tip4p  1e-4

neighbor	      2 bin
#neigh_modify     exclude type 3 3 
neigh_modify     delay 0 every 1 check yes


min_style cg
minimize 1.0e-4 1.0e-6 100 1000
#minimize 1.0e-6 1.0e-6 1000 10000


group solvent type 1 2
group cnt type 3





velocity solvent create 298.0 12345678 dist uniform  #Apply Nose-Hoover termostate on water molecules



delete_atoms overlap 0.3 solvent cnt mol yes

region   trash cylinder z 20 20 6.9 1 41 units box side out #7.54
group trash region trash
delete_atoms overlap 0.5 trash cnt bond yes



####################
fix 1 solvent nve/limit 0.1
fix 2 solvent langevin 298.0 298.0 1000.0 699483 
fix 3 solvent nvt temp 298.0 298.0 100
fix 4 solvent npt temp 298.0 298.0 100.0 iso 0.0 0.0 1000.0
#####################


fix push cnt nve
velocity cnt     set 0 0 0 units box
fix NOFORCE1 cnt setforce 0 0 0


thermo 100 
thermo_style custom step temp pe ke etotal
log logequi.txt  


dump 1 all custom 1000 dump.lammpstrj id type x y z 
write_data output.data
run 10000 # 100000