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Project updates

JCl

Past week:

• TM-FF

  • Created draft of plan and ran it by Chris Iacovella

  • Expect meeting with Genentech when Richard is back at the end of the month. Monthly meeting with Genentech and off biweekly without them.

  • Worked with Chris to separate properties of primary and secondary importance.

    • Those of primary importance should come from single point calculations, but not all seem accessible from QCA

    • Those of secondary importance require a freq calculation and are of scientific not FF dev interest and so are not a priority

• Replicating calculation issue:

  • First sage 2.0 opt merged and created new records. Need to resolve before merging other datasets

  • create test that new records will be made, maybe a flag, generate_new_records=False?

  • Sage 2.0 TD ready and waiting

  • Sage 2.1 combined Opt and TD (ensure this works properly before preparing Sage 2.2)

• Dataset Longevity

  • Ben is working on making “views” of these files (HDF5) available server side to download and wonders if we are interested. We could request the server create these files from a dataset and upload them to an S3 bucket (or some other S3 compatible storage). These would be then attached to the dataset and downloadable with QCPortal

    • Chris says that this was standard functionality before the major upgrade and if very useful, although is concerned that QCA is supposed to be a living database and these views are static snapshots.

  • Ben also recommended a downloader script that Peter Eastman created.

    • Chris has worked with this downloader and parallelized it. The script as is takes 19 hr to download SPICE2 but with Chris’ version it takes 1.5 hrs.

    • Chris said that Ben already added something to download files with SQL and they are planning to use that

    • Chris has a repo that he is refining to allow them to only pull the information they need for fitting. Given the overlap in interest, I expressed that we are interested in collaborating on this and will likely reach out to see what he has.

Next week:

• TM-FF

  • Debug failing opt for Brents TM database

  • Work on exposing needed single point properties

  • Finalize project plan, in ZenHub?

• Replicating calculation issue:

  • create test that new records will be made, maybe a flag, generate_new_records=False?

• Dataset Longevity

  • Set up meeting with Chris and Ben, either together or separately.

Project updates

LW

• Past week:

  • Looking into Evaluator liquid simulations

  Next week:

  • Setting up EquilibrationLayer and PreequilibratedSimulationLayer technical workflow in Evaluator

• This/next week:

  • Figuring out sensible default kwargs for Evaluator (primarily around equilibration times and conditions)

  • Trialling several use cases

    • fitting a FF (projects: NAGL, DCole)

    • benchmarking across water models (stakeholder: Shirts group)

  • Working out hand-off to infrastructure team ( ? ) and what to do about current gaping holes in code

  • Debugging protein benchmarks