2022_06_27 Core Devs

General updates

• JW – Annual meeting is tomorrow, in 30 minutes. I may recruit people as co-hosts to help police the audience.

• CC – I’ll be offline next week

Individual updates

• MT

  • Tried to make an example for the annual meeting but had trouble.

  • Merged a PR to update examples, split examples that require ParmEd and OpenMMForceFields into an examples/external/ subfolder. This is a compromise position, as I don’t want us to have anything to do with those two packages.

  • Preparing for a gromacs update - Working on understanding assumptions, like whether two isomorphic molecules should get identical parameters assigned.

  • Found some performance improvements for gromacs export.

• DD

  • fah-alchemy

    • worked with Gowers and Swenson on storage front last couple weeks; approach to storage appears largely settled in gufe

    • implemented S3 storage backend in gufe: https://github.com/OpenFreeEnergy/gufe/pull/34

    • moving on to working on specific protocols in fah-alchemy

  • QCArchive

    • Working with clusters that have had high throughput - Completing a lot of optimizations.

  • Haven’t had a chance to return to the QCSubmit refactor in response to new QCFractal release.

• CC

  • Offline most of last week.

  • Keeping backburnered things going -

    • QCF 3-mer torsiondrive datasets. These are getting enar the number of opts/torsiondrive that the previous set required to converge, so we may be near completion.

      • DD – Once we start seeing diminishing returns, I can help figure out how to advance these toward completion.

    • Working on grant with Gilson and Mobley for conformer generation for small molecules/natural products using NMR data.

    • Set up a meeting with alnylam on weds, they do nucleic acid stuff.

• JW

  • Annual meeting planning

    • Preparing slides

    • Defining strategy - Basically making a projection of our WBSes that are intended to be consumed by high-level external observers rather than staff.

    • Coordinating with other speakers.

    • Coming up with practices about how to invite/inform/manage webinar attendees.

  • F@H/OpenFE coordination

    • Question about stable, long term reverse-compatible OFFMol serialized format. They want stable versioned core representations that can be loaded into the future.

  • Worked on OE protein loading a little.

  • Working on substructure loading/definition

• PB

  • Some work on getting the DEXP-optimized FF's valence parameters refit, some targets are failing in the first step itself so have to spend some more time on filtering those or tuning hyperparameters.

  • Dataset resubmission with additional mols for Jessica's set of torsions.

  • Reviewing first draft of Sage manuscript, sending it out to Mobley and Shirts for intermediate review this week.

  • Updating documentation on confluence.

• DN

  • Excited for annual meeting tomorrow, and to share my thoughts on strategy. In other roles I’ve guided strategic planning for large teams. There are three principles: Putting the right people in the right places, building a good organizational culture, and repeating the key points of this culture on a daily basis. It’s important for us to be self-directed, and now tweaking the project and its goals every day. So the strategy will protect us from shifts in scope/priority.

  • Drafting annual report - I’ll be totally focused on this after the annual meeting, so please look for questions from me after Tuesday, since this document will help people advocate for us in their companies.

•  

•  

•