kspace_style pppm 0.0001
kspace_modify slab 3.0

read_restart rst.lambda0.2950000


#group hydrophobic and hydrophilic

group phyl type 3 4 6 7

group phob type 1 2 5

#group water

group water id 12275:19414
group water_o id 12276:19413:3
group water_h subtract water water_o
group sulfur type 3
group oxy_c  type 2


#fix wall on top and bottom

fix wallphob phob wall/lj93 zhi EDGE 0.25 3.2 15 zlo EDGE 0.25 3.2 15

fix wallphyl phyl wall/lj93 zhi EDGE 1.5 3.2 15  zlo EDGE 1.5 3.2 15

fix_modify wallphob energy yes
fix_modify wallphyl energy yes


neighbor        2.0 bin
neigh_modify every 1 page 150000 one 5000


thermo 100
thermo_style custom step temp epair emol etotal press vol density
timestep        1.0  # femtoseconds

restart 50000 rst.lambda0


# saving trajectory

dump  Datom1 all custom 5000 dump.lambda0 id type xu yu zu ix iy iz
dump_modify Datom1 sort 1

dump  Datom2 all custom 5000 dump.lambda1 id type x y z ix iy iz
dump_modify Datom2 sort 1


#npt run

fix npt2 all npt temp 300 300 50 x 1 1 100 y 1 1 100 couple xy drag 2.0

run 5000000
unfix npt2

undump Datom1
undump Datom2

# saving trajectory production

dump  Datom3 all custom 500 unwrap.lammpstrj id type xu yu zu ix iy iz
dump_modify Datom3 sort 1

dump  Datom4 all custom 500 wrap.lammpstrj id type x y z ix iy iz
dump_modify Datom4 sort 1

#number density

compute water_o_chunk water_o chunk/atom bin/1d z lower 0.2 units box
compute water_h_chunk water_h chunk/atom bin/1d z lower 0.2 units box
compute sulfur_chunk sulfur chunk/atom bin/1d z lower 0.2 units box
compute oxy_c_chunk oxy_c chunk/atom bin/1d z lower 0.2 units box

fix water_o_density water_o ave/chunk 10 10 500 water_o_chunk density/mass density/number ave running file water_o_density.txt format %20.2g
fix water_h_density water_h ave/chunk 10 10 500 water_h_chunk density/mass density/number ave running file water_h_density.txt format %20.2g
fix sulfur_density sulfur ave/chunk 10 10 500 sulfur_chunk density/mass density/number ave running file sulfur_density.txt format %20.2g
fix oxy_c_density oxy_c ave/chunk 10 10 500 oxy_c_chunk density/mass density/number ave running file oxy_c_density.txt format %20.2g


#npt production run

fix npt3 all npt temp 300 300 50 x 1 1 100 y 1 1 100 couple xy drag 2.0

run 2000000
unfix npt3