# LAMMPS input for HTMB equillibration # MF, 06-19-2012 #------------------------------------------------------------- # INITIALIZATION #------------------------------------------------------------- units real dimension 3 newton on on boundary p p p atom_style full neighbor 2.0 bin neigh_modify delay 0 every 1 check yes one 5000 page 100000 #------------------------------------------------------------- # ATOM DEFINITION (FORCEFIELD: OPLS) #------------------------------------------------------------- read_data data.CH3OH #------------------------------------------------------------- bond_style harmonic bond_coeff 1 553.0000 0.9450 bond_coeff 2 340.0000 1.0900 bond_coeff 3 320.0000 1.4100 #------------------------------------------------------------- angle_style harmonic angle_coeff 1 33.0000 107.8000 angle_coeff 2 100.0000 126.0000 angle_coeff 3 35.0000 109.5000 #------------------------------------------------------------- #pair_style buck/coul/long 12.5 #pair_coeff 1 1 125652.45683 0.25429 555.73878 #pair_coeff 1 2 0.00000 1.00000 0.00000 #pair_coeff 1 3 52784.58984 0.22763 120.10556 #pair_coeff 1 4 78292.19907 0.26933 488.83080 #pair_coeff 2 2 0.00000 1.00000 0.00000 #pair_coeff 2 3 0.00000 1.00000 0.00000 #pair_coeff 2 4 0.00000 1.00000 0.00000 #pair_coeff 3 3 22173.96297 0.20376 25.95706 #pair_coeff 3 4 32889.30213 0.24109 105.64549 #pair_coeff 4 4 48782.71854 0.28526 429.97818 #------------------------------------------------------------- pair_style lj/cut/coul/long 12.5 pair_coeff 1 1 0.1700 3.1200 pair_coeff 2 2 0.0000 0.0000 pair_coeff 3 3 0.0300 2.5000 pair_coeff 4 4 0.0660 3.5000 pair_modify mix geometric #------------------------------------------------------------- special_bonds lj/coul 0.0 0.0 0.5 kspace_style pppm 1.0e-6 #------------------------------------------------------------- dihedral_style opls dihedral_coeff 1 0.0000 0.0000 0.3520 0.0000 #------------------------------------------------------------- # setup simulation: #------------------------------------------------------------- run_style verlet timestep 0.1 reset_timestep 0 thermo_style custom step temp press vol etotal pe ke emol ebond eangle edihed epair evdwl ecoul elong thermo 1000 # restart 1000 restart.CH3OH dump 1 all custom 1000 frame.*.dmp id mol type x y z vx vy vz dump_modify 1 format "%10d %6d %4d %15.10g %15.10g %15.10g %25.20g %25.20g %25.20g" sort id #------------------------------------------------------------- # run part 1: push-off #------------------------------------------------------------- fix 1 all nve/limit 0.1 fix 2 all temp/rescale 100 298.15 298.15 10.0 1.0 run 50000 unfix 1 unfix 2 #------------------------------------------------------------- # run part 2: NVT #------------------------------------------------------------- fix 1 all nvt temp 298.15 298.15 10 run 50000 unfix 1 #------------------------------------------------------------- # run part 3: NPT #------------------------------------------------------------- fix 1 all npt temp 298.15 298.15 10 iso 1.0 1.0 100 run 100000 unfix 1