# DRIVER SCRIPT units real atom_style full # FORCE FIELD SET UP pair_style lj/charmm/coul/long 15.0 18 # using extra-long cut-off to compare with hand calc bond_style harmonic angle_style harmonic dihedral_style charmm kspace_style ewald 0.0001 pair_modify mix arithmetic # SPECIAL BONDS #special_bonds charmm special_bonds lj 0.0 0.0 0.0 coul 0.0 0.0 0.0 dihedral yes # DATA FILE read_data data.charmmLJ # RUN SETTINGS neigh_modify delay 2 every 1 timestep 1.0 velocity all create 300.0 12345678 dist uniform fix 1 all nve thermo_style multi thermo 1 compute pePerAtomID all pe/atom pair # DUMPS dump 1 all atom 10 dump.all # unscaled coordinates ( atom_ID molecule_ID x y z ) dump dumpIdxyz all custom 1 dump.xyz id mol x y z # per atom pe computed above using ID = pePerAtomID dump dumpIdpe all custom 1 dump.pePerAtomID c_pePerAtomID run 1