How to create a periodic crystal structure with lots of angle, dihedral and improper interactions efficiently

LAMMPS LAMMPS Beginners
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There is an alternative way to create a viable topology for molecular crystals with bonds crossing the periodic boundaries, discussed in this mailing list thread and based on the software Moltemplate. To summarise:

  1. Create a supercell by replicating the unit cell (CIF or PDB) with your favourite tool. Mine is GDIS, available in almost every Linux distribution.
  2. Open the supercell (exported as a PDB) in VMD and use the topotools to create the bonds based on the distance.
  3. Export the structure plus bond connectivity to a LAMMPS data file.
  4. Convert the data file to a LT file with ltemplify.py.
  5. Add the force field terms for angles, impropers, and dihedrals to the LT file. Please refer to the “Bonded interactions by type” section of the Moltemplate manual.
    The method suggested implies familiarity with Moltemplate. Start by running some of the examples to get started, especially the ones on polymers.
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