units              real
atom_style         full
dimension          3
newton             on
boundary           p p p 

bond_style         harmonic
angle_style        harmonic
dihedral_style     opls
improper_style     cvff
pair_style         lj/cut/coul/long 12.5
pair_modify        mix geometric shift yes
kspace_style       pppm 3.0e-5
special_bonds      lj/coul 0.0 0.0 0.5

read_data          final.lmps
group H2O type     28 29 30
group poly subtract all H2O
group hydroxide type 26

# Settings
dielectric         1.0
neighbor           2.0 bin
neigh_modify       delay 0 every 1 check yes page 10000000 one 10000
timestep           1
run_style          verlet


dump               1 all custom 10000 product1.lammpstrj id type xu yu zu vx vy vz ix iy iz
thermo_style       custom step density vol temp press pe etotal evdwl ecoul ebond eangle edihed eimp
thermo             1000


compute            mymsd hydroxide msd

####################################################################
velocity           all create 300 58447419
run                0 
velocity           all scale 300

fix                myrigid H2O rigid/nvt/small molecule temp 300 300 100
fix                1 poly nvt temp 300 300 100
fix                2 poly ave/time 100 1 10000 c_mymsd[*] file msd_data1.txt ave running
run                100000

unfix              2
unfix              1
unfix              myrigid
####################################################################
# Output
write_data         product.lmps