# 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       config.data extra/atom/types 1 

bond_style harmonic	
bond_coeff 1 469.0  1.0     #H-O


angle_style harmonic
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-4
#kspace_style pppm/tip4p  1e-4

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

#delete_atoms overlap 0.3 all all

group solvent id  <> 1 13200

fix rigid solvent shake 1.0e-6 500 0 b 1 a 1

fix NVT solvent nvt temp 298.0 298.0 100      #Apply Nose-Hoover termostate on water molecules

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





#group cnt id <> 28417  29096  ######



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


dump 1 all custom 10000 dump.lammpstrj id type x y z 
run 100 # 50000
undump 1
##################

reset_timestep 0

#region mybox block -0.2 50.2 -0.2 50.2 -0.2 60.2 
#create_box 3 mybox bond/types 2 angle/types 1

read_data cc.data  add offset 3 1 0 0 0 group cnt

pair_coeff     3  3     0.07    3.9848     #C-C
pair_coeff     1  3      0.0     1.9924     #H-C
pair_coeff     2  3      0.104264     3.5754     #O-C

region trash cylinder z 25 25 6.77 1 60 units box side out
group trash region trash
delete_atoms group trash

region   cyl cylinder z 25 25 6.77 1 60 units box
group cyl region cyl

delete_atoms overlap 0.3 solvent cyl
group H2O type 1 2
fix 1 H2O nve/limit 0.1
fix 2 H2O langevin 1.0 1.0 1000.0 699483 
fix 3 H2O nvt temp 298.0 298.0 100
fix 4 H2O npt temp 298.0 298.0 100.0 iso 0.0 0.0 1000.0

thermo 1000 
thermo_style custom step temp pe ke etotal
log logequi2.txt 

dump 2 all custom 10000 dump2.lammpstrj id type x y z 
run 5000 # 50000