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Project updates

BW

• Next 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)

  • Organometallics dataset

    • JW gave go-ahead to submit mols that made it through the toolkit. Brainstormed how to handle CIF file

    • Brainstormed ways to bypass the toolkit and get data to QCArchive

  • yammbs/YDS torsions

  • • • ~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 equalLW: to paste weights-checking script

    • 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

    • Github link macro
      link https://github.com/openforcefield/proteinbenchmark/blob/main/proteinbenchmark/benchmark_targets.py

    • 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

      • paid GPU queue on HPC3, request a week or two

      • gpu

        • dmobley_lab_gpu

        • LW: to send BW a script

      • free-gpuOpenMM 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:

      • Github link macro
        link https://github.com/bismuthadams1/nagl-mbis

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 – maybe passing 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