# Program to equilibrate water #TIP3P water #Simulation Units andSimulation Type boundary p p p restart 100000 restart.water units real atom_style full #Reads configuration from file read_data /userdata/nandu/fftwtest/waternew.txt #read_restart restart.water.* group hydrogen type 1 group oxygen type 2 group water type 1 2 set group oxygen charge -1.04844 set group hydrogen charge 0.52422 #Define potential type pair_style lj/charmm/coul/long 10.0 12.0 12.0 kspace_style pppm 5.0e-5 kspace_modify mesh 36 36 36 order 5 pair_coeff 2 2 0.1521000000 3.15061 pair_coeff 1 1 0.0000000000 0.000 pair_coeff 1 2 0.0000000000 0.000 angle_style harmonic angle_coeff 1 55 104.52 bond_style harmonic bond_coeff 1 450 0.9572 velocity all create 375 234324 dist gaussian loop local neighbor 6.0 bin neigh_modify delay 0 page 200000 one 10000 minimize 1.0e-4 1.0e-6 100 1000 #thermo_style custom step pe ke etotal temp press #Applies or "fixes" fix a all nve fix 1 water shake 0.0001 20 500 b 1 a 1 #Dumps output files and thermodynamic properties #dump 1 all custom 100 dump.water mol f_prob thermo 500 #Timestep is 1 fs (0.001 ps) timestep 1 #Number of time steps (reduced) run 100000 unfix a compute mobile all temp compute pres all pressure mobile fix b all npt temp 375 375 100 iso 1.0 1.0 1000 fix_modify b temp mobile press pres run 80000 unfix b fix c all nvt temp 375 375 100 fix_modify c temp mobile run 40000 unfix c fix d all nve compute msdmol water msd/molecule fix f all ave/time 1 100 100 c_msdmol[3] mode vector ave running file amma.txt variable a atom pe variable b atom ecoul variable c atom evdwl variable d atom elong variable e atom etail variable f atom epair compute aveenergy water reduce ave v_a compute coulom water reduce ave v_b compute vander water reduce ave v_c compute long water reduce ave v_d compute tail water reduce ave v_e compute pair water reduce ave v_f fix energy water ave/time 1 100 100 c_aveenergy c_coulom c_vander c_long c_tail c_pair ave running file energy.txt compute peatom water pe/atom fix prob water ave/atom 1 100 100 c_peatom dump 1 all custom 100 dump.waterprob mol f_prob compute energies water atom/molecule v_a fix energies water ave/time 1 100 100 c_energies file energies.txt mode vector run 320000