2022-01-26 Thompson/Wagner Check in

General updates

• Feedback on Interchange rollout project plan

  • (JW and MT discussed, JW commented on places in our code that should specify use_interchange=False)

• MT – I need test molecules and FF for vsites

  • JW – This should be pretty straightforward, except that I need to come up with cases that exercise the match keyword values, wildcards in SMIRKS, and parameter collisions with or without matching names, and those are super confusing.

    • MT – This is super confusing. It would be good to loop in SB on the design of these tests.

  • https://open-forcefield-toolkit.readthedocs.io/en/latest/users/virtualsites.html

• JW planned agenda items:

• Show res info defined/undefined to/from OMM/RDKit/OE spec Planning to add somewhere in docs, along with other core props <https://github.com/openforcefield/openff-toolkit/issues/135> Need eyes on anything?/PR clearance

PR clearance/issue discussion

• MT – Found an issue with elements to masses

  • (Discussed in , ultimately decided to have our own dict of atomic number to mass and symbol, which will live in openff-units)

• MT – Finding charge (and other thing) differences in regression suite

  • JW – Possibilities are:

    • Changes in use of normalize_partial_charges kwarg - This doesn’t seem to be the case, and frequently the differences are too large to be explained by this

    • Changes in the topology refactor branch - We could test this by running create_openmm_system in the refactor branch with use_interchange=True/False

      • MT – I’ll start here tomorrow

    • Omega generating different conformers? Could test by running the same set twice with the same program version.

    • Some change in how aromaticity is perceived/assigned/preserved? Not sure how to test this, or what effect it’d have.