2021-06-22 VSite architecture meeting notes

Architecture of VSites

• JW – Are vsites assigned parameters, or part of a topology?

  • Assigned parameters

    • They’re created by the parameter assignment step

    • They can’t have their coordinates meaningfully set by users

  • Part of topology

    • Output formats expect them to be listed as particles

    • Users probably want to ASK them what their coordinates are

  • JW’s vote: They’re assigned parameters

• JW – Should vsites be allowed to be set pre-parameterization?

  • Pre-parameterization vsite creation is most closely analogous to charge_from_molecules – Is there a similar pattern that we can follow to LibraryChargeType.from_molecule to make vsite parameters from a molecule with vsites? Or something like that interface?