Increasing simulation box makes bond error

LAMMPS LAMMPS Beginners
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Please see this recent discussion for some strategies that you may be able to adapt for your case.

Another possible procedure:

  • use write_dump to write out unwrapped coordinates
  • use set command to set all image flags to 0
  • use change_box to change your box dimensions
  • use read_dump with box no to read back the coordinates, but retain the enlarged box
  • use reset_atoms image to reset image flags for the dump data while keeping molecules intact
  • use write_data to write out the updated system as data file
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