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Participants

Discussion topics

Item

Notes

Task planning

  • Can move ahead with reference dataset, even if some details aren’t hammered out in the SMIRNOFF spec – Lots of peolpe just want to know if they’re getting torsions right, don’t care as much about precise agreement with long-range forces

  • Capping+charging unrecognized AAs in a protein.

    • LibraryChargeHandler.unrecognized_contiguous_subgraphs → list of tuple of atom indices?? Then we could have a way to turn those subgraphs into capped mols, assign charges, and turn them back into LibraryCharges??

    • May be good to get interface hints here from LWang’s polymeterizer

  • Interchange importers?

    • MT – Blocked by lack of TypedMolecule, could use mdtraj top as a crutch for now.

    • MT – Concerned about scope creep. Some things are black and white - Loading a prmtop that uses ff03 should clearly be allowed, loading a prmtop wiht an unsupported vsite is clearly not our job (though folks are free to open PRs). But there’s a significant grey area around things like loading CMAPs from prmtop.

  • Test usage of graphlib instead of networkx for heavy comparisons in Toolkit

    • is/are_isomorphic → Relatively cheap, ok to be inefficient. Only expected to match entire molecules. SHOULDN’T try to match subgraphs. Less important to remove networkx here.

    • Molecule.from_pdb → Very expensive, could be sped up a lot. Needs to match subgraphs (individual residues in a larger chain). Important to find something faster than networkx here.

  • Somehow improve SMARTS based parameter assignment for proteins. This would be really easy with multiprocessing, but that’s the last tool I want to reach for.

Units PR

  • MT – When can we stop supporting simtk.units? It adds a good amount of complexity to openff-units.

    • JW – Let’s stop supporting it in the Feb release.

  • JW will finish reviewing this on his own time – Logic looks good, will just act a s a second set of eyes for typos. If #1097 look good, we will close it and merge #1142, since it’s the same logic, just ported to the topology-refactor branch.

Topology performance/molecule grouping merge

  • MT reviewed #1140, JW merged

Pushing molecule grouping updates into interchange

  • MT will work on bringing similar performance improvements to those in #1140 into interchange

Topology-export-to-different-format needs

Resolving positions debate

  • How many conformers can a molecule have?

    • One?

      • Direct correlation to simulation coordinates

    • Multiple?

      • Allows ELF10 work

    • Unresolved - Opened to debate on #developers channel

  • Can a Topology have conformers?

    • No

  • What is the relationship between interchange positions and molecule conformers?

    • Interchange positions will be totally separate

Action items

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Decisions

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