units real boundary p p p atom_style full bond_style harmonic angle_style harmonic dihedral_style opls improper_style none pair_style lj/cut/coul/long 12.0 read_data t-2remain.data pair_modify mix geometric # special_bonds lj/coul 0.0 0.0 0.5 special_bonds lj/coul 1.0 1.0 1.0 kspace_style pppm 5.0e-5 thermo 1 thermo_style custom step cpu temp press evdwl ecoul emol lx ly lz thermo_modify flush yes timestep 1.0 #################################### group mol1 molecule 1 group mol2 molecule 2 #################################### delete_atoms overlap 12 mol1 mol2 mol yes neighbor 2.0 bin neigh_modify every 1 delay 1 check yes balance dynamic xyz 30 1.0 write_data t-deleted.data write_restart t-deleted.rst