# -- Init Section -- include system.in.init # -- Atom Definition Section -- read_data system.data # -- Settings Section -- include system.in.settings # -- Run Section -- timestep 1.0 dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz thermo_style custom step temp pe etotal press vol epair ebond eangle edihed thermo 500 # time interval for printing out "thermo" data # Improve efficiency by not calcuating interactions between immobile atoms neigh_modify exclude group groupB groupB # Now move the remaining atoms (all except groupB) group mobile subtract all groupB fix 1 mobile nvt temp 300.0 300.0 100.0 run 100000 write_restart system_after_nvt.rst