2021-01-27 Benchmarking for Industry Partners - Development Meeting notes

Updates

• DH: test calculations (non-burn-in)

  • hitting a lot of “Unknown error” cases; may try option (c) and see if this produces different results

    • these do appear to reduce in number after each error cycling, so not easy to reproduce in a single case

  • DD: if there are any persistent error cases after several rounds of error cycling, please share (if you can) the input molecule and we can take it to the psi4 devs to get a better solution in place (at least better error messaging)

• JW: worked on deployment last week; making conda package (automation), implementing single-file installer (automation)

  • tricky bug in RDKit; seen references by Greg Landrum

    • in validation, when a mol passes other checks, later on the mol will get written and read in SDF

    • there are cases where there is not full fidelity in write/read; we do this as part of our validation for this reason; write to a StringIO object to avoid hammering filesystem

    • there are some cases that roundtripping StringIO fails, but to a file does not. Is consistently reproducible for a given molecule that fails; not clear what about these molecules is causing this

    • so, switched to using filesystem writes instead of StringIO to avoid the issue for now; will pursue (later) creating an RDKit issue with an example

  • also found a mangling of the atom indices from QM output

    • QM export is the first place we see it

    • have ideas on where the problem is; will investigate and report back findings

  • working to make parameter coverage output (step 3) be the input for optimizations (step 4)

  • have two places where we use arbitrary RMS cutoffs

    • minimum allowable RMS between generated conformers (step 2): 1.0A

      • propose changing to 1.5A

    • deduplication for input conformers (step 1): 0.1A

      • propose changing to 1.0A

    • the proposed changes would reduce the number of conformers in a dataset, speeding up the QM stage of the benchmark globally

    • the existing choices give more conformers, and differences between them are perhaps not meaningful at the level of our forcefield

    • [decision] change input conformer deduplication cutoff from 0.1 to 1.0A heavy-atom RMS; change conformer generation cutoff from 1.0A to 1.5A heavy-atom RMS

      • Jeff will make this change as a PR; David H. will give it a go to see how many molecules come through from his testing dataset

        • need to make sure we don’t end up with e.g. over 50% of molecules with only one conformer

• JH: had a go at the burn-in set; will use to investigate issues with Jeff

  • played around with psi4 versions; resolved

  • we should follow up with Ben and ask about psi4 release schedule plans

• DD:

  • need to create group codes for each partner

    • BASF : BSF

    • VRTX : VTX

    • XTALPI : XTP

    • BMS : BMS

    • MERCK : MRK

    • BOEHRINGER-INGELHEIM : BRI

    • ROCHE : RCH

    • GENENTECH : GNT

    • BAYER : BYR

    • JANSSEN : JNS

  • working

Burn-in

David D.

• DD: how do we poke partners to get feedback?

• JW: we’ll run out of bandwidth if we resort to DMs; best to keep it on the channels

  • resort to DM threads with all of us on it if needed, but only if asked

• DD: will draft a “poke” message for #benchmarks-partners, send to JW,JH,DH as draft

• DD: will prepare a spreadsheet of all partners, with status indicators like “burn-in complete”, “started production run”, “choice of optimization approach”, “variation notes”

Project risks