2024-12-03 Science team meeting

Project updates

BW

• Next 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

  • Protein fits

    • check weights and resubmit if they aren’t equal

    • LW: to paste weights-checking script

  • nagl2

    • combine opt datasets into one

    • basic dataset from combined dataset

      • same props as mlpepper

      • save wavefunction

• Next week

  • More benchmarks

  • 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

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

      • gpu

        • dmobley_lab_gpu

        • LW: to send BW a script

      • free-gpu

    • 3 replicates to start with

LW

• Past week:

  • Mostly off sick

• Next week:

  • Evaluator on Kubernetes – maybe passing off to Matt

  • Liquid simulation validation

    • thermostats are not regulating temperatures

    •