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Presenter

Notes

Project updates

BW

  • Last week

    • More benchmarks

      • v3 besmarts

      • null-looser-priors protein ff

      • null-0.0.3

    • QCA workers

      • 1x Hessian datasets still going (protomers)

      • lipid-maps-medium

      • lipid-maps-large (on virginia tech)

        • ~1% finished in 3 days across 1 node, 24 cores/job, 90 GB memory/job. Large ones seem to be using ~70 GB RAM

        • Molecules may be too large

    • Organometallics dataset

      • Waiting until QCA workers free up to merge

    • Protein fits

      • check weights and resubmit if they aren’t equal

      • BW: 47% Opt, 26% SM TDs, 27% proteins

    • nagl2

      • combine opt datasets into one

        • AMI came back and did this

      • basic dataset from combined dataset

        • same props as mlpepper

        • save wavefunction

      • Protein fit benchmarks

  • Next week

    • More benchmarks

      • v3 besmarts

    • QCA workers

    • Second lipidmaps dataset

    • Organometallics dataset

    • yammbs/YDS torsions

    • Protein fits

      • LW: in benchmark_targets.py – would recommend setting traj_length to 5 microseconds (in a new target) instead of 10, for purposes of speed. We should be able to extend the trajectory fairly easily later

        • OpenMM exception: NaN coordinate

        • LW: restart again? Otherwise I’ll see if I can visualize anything obviously wrong in VMD

        • /dfs9/dmobley-lab/bwestbr1/proteinbenchmark/output/results/gb3-test-5us-null-looser-priors-tip3p/setup

        • /data/homezvol0/bwestbr1/mambaforge

      • 3 replicates to start with

      • DCole NAGL repo:

Project updates

JCl

Past week:

  • Onboarding

    • Working with JW on CMILES issue in existing datasets

      • In RDKit, some CMILES turn out as radicals but don’t result in errors. However, will error in OpenEye. Trying to add an error to catch this scenario from RDKit

    • Radicals with SMILES is a question mark – will we have to think about this with organometallics project?

      • More in future work

  • Next week:

    • Working more on CMILES issue

    • Dataset release stuff

Project updates

LW

  • Past week:

    • Mostly off on leave!

    • Evaluator on Kubernetes – passed off to Matt

    • Liquid simulation validation

      • thermostats are not regulating temperatures

  • Next week:

    • Looking into Evaluator liquid simulations

    • Working with Matt on Kubernetes

    • Protein benchmarks

    • Picking up everything that happened on leave

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