# when units=real use units length:Angstrom (A), time:femto second(fs), Temperature: Kelvin(K),Energy:Kcal/mol, Presuure:atm units real dimension 3 boundary p p p processors 4 4 3 atom_style full bond_style harmonic angle_style harmonic special_bonds lj/coul 0.0 0.0 0.5 #comment for production run read_data /p/home/sbekele/BulkWater/dat.water.swm4-ndp #read_restart restart_30A30A30A.100000 pair_style lj/cut/coul/long 12.5 12.5 #pair_modify tail yes kspace_style pppm 1e-5 pair_coeff 1 1 0.210939 3.183950#O-O pair_coeff * 2* 0.0000 0.0000 #H-H, O-H #bond_coeff 1 550.0 1.000 #angle_coeff 1 900.0 109.47 group ATOMS type 1:3 group CORES type 1 group DRUDES type 4 variable TK equal 300.0 variable TDK equal 1.0 variable PBAR equal 1.0 #extra distance beyond force cutoff neighbor 3.5 bin #update neighbor list neigh_modify delay 0 every 1 one 3000 #page 100000 fix DRUDE all drude C N N D velocity ATOMS create ${TK} 12345 velocity DRUDES create ${TDK} 12345 delete_bonds ATOMS multi comm_modify vel yes compute TATOM ATOMS temp/com compute TEMP all temp/drude fix MOMENTUM all momentum 100 linear 1 1 1 #NPT ensemble using Nose-Hoover thermostat: fix DTDIR all drude/transform/direct fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500 fix_modify RIGID temp TATOM press thermo_press fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0 fix DTINV all drude/transform/inverse timestep 1.0 thermo_style custom step etotal pe ke ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2] #thermo_style multi thermo 1000 #(adjust this number to get write TotEng etc. data to log file, say evey 100 fs) thermo_modify flush yes restart 20000 restart_swm4nh_npt12.5 #equlibration runs #npt runs dump 1 all custom 1000 /p/home/sbekele/BulkWater/atom_npt_swm4nh_12.5 id type mol xs ys zs ix iy iz run 100000 unfix DTDIR unfix RIGID unfix NVT unfix DTINV undump 1 #NVT ensemble using Nose-Hoover thermostat: fix DIRECT all drude/transform/direct fix RIGID ATOMS rigid/nvt/small molecule temp 300. 300. 100 fix NVT DRUDES nvt temp 1. 1. 20 fix INVERSE all drude/transform/inverse timestep 1.0 restart 50000 restart_swm4nh_nvt_12.5 dump 1 all custom 1000 /p/home/sbekele/BulkWater/atom_nvt_swm4nh_12.5 id type mol xs ys zs ix iy iz run 1000000