2024-04-17 Meeting notes

Feature requests

LW

• MT – Both discussed in issues that LW opened:

  • Slice benchmark results by parameter

    • MT – Could be handy if you have existing code that does this/shows what you want.

    • LM – So far, I do SMIRKS search of QM dataset to build these filtered sets. BW also had something that slices by parameter.

      • https://github.com/ntBre/benchmarking/blob/0e27189c9334a6aa4176b86cc986d7450d7a9328/misc/triage.py

    • BW – Yeah, I go through QCA IDs and search by SMILES. This would seem to be best as a post-processing step, since otherwise it’d just use a lot of disk space.

    • MT – We could implement tagging by parameter, or searching by SMIRKS. Wasn’t thinking of storing this in database, rather a second location.

    • LM – Yeah, agree this would be best in post processing.

    • JW – Is OFFMol I/O being slow an issue here? I’ve put very little work into optimizaing this.

    • BW – My normal thing is to … Takes 45 mins on 9800 mols.

    • LW – 45 minutes is a bit long, 5 minutes wouldn’t be bad

    • …

    • (slow part is molecule.from_smiles

    • JW – 5 min for 10k mol is quite slow for toolkits like RDKit. It might be easier to not go through OpenFF

    • BW – I’d tried using RDKit before but there was lots of back-and-forth

    • LW – slow/hard part was kekulizaton

    • BW – I use addhs, sanitize

    • LW (irrelevant side note): – ff.label_molecules(Topology.from_molecules[]) could be hacked to create a super RDKit mol that could be labelled all at once

  • Torsion-constrained data

    • It’ll be in this repo (for torsion constrained minimization):

• Brent’s code for parameter stuff:

• LW – I’ll link some code snippets to do this. The first item above would be really handy.

  •  

  • MT –

• LW – Also, a related feature request would be to invoke checkmol for slicing. Checkmol is funcitonality that groups mols by functional groups.

  • LM – I haven’t used that but it sounds good.

• https://openforcefieldgroup.slack.com/archives/C03T3LLVC1J/p1713340639866169?thread_ts=1713285654.391259&cid=C03T3LLVC1J

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Trello update

MT

https://trello.com/b/dzvFZnv4/infrastructure?filter=label:benchmarking

Lessons learned re: 2.2 release benchmarking

JW

•  

• JW - worth re-doing comparisons between versions of benchmarking code (using the same data)?

  • (This in comparison to re-running old data (like 2.0) whenever the benchmarking code changes)

    • LM - I expect re-running 2.0 data to be pretty much the same if using new code (YAMMBS 0.0.7 compared to Simon/Pavan) now that QM minima is used for DDE (this at least for the DDE numbers)

    • JW – do we have the CSV for the old benchmarking data so we can compare?

    • LW + LM – I believe the data is in the sage release notes

  • JW – And can we check for agreement on SFE benchmarks?

    • MT – 100-200 solute-solvent combos were used previously. a

      • Here’s the SFE data used in the 2.0 paper:

      • Phase 1 of validation is MO will use the new code and 10 combos as a validation set for the new code (the stuff I’m contributing to OpenFE skunkworks).

        • MT/RG discussion putting together the targets for validating skunkworks: 2024-04-03 OpenFF/FE collab

      • Phase 2 could be rerunning the SFE calcs that were done for a previous FF, and we could compare to that in the future if we wanted.

    • (General) – The convergence criteria may have always been extremely strict. Even in industry benchmarking, even in forcebalance(?)

      • https://github.com/openforcefield/openff-evaluator/issues/530

  • LW – Most of the issues seemed to be around qcsubmit, QCA, and other tools, not much ended up being with YAMMBS.

    • LM – A big problem was with timeouts from QCA. Another big problem was with DASK doing charge checks. But I solved both of those (and can share solutions if needed!)