2025-01-21 All-hands meeting notes

Infrastructure Updates

JW

https://docs.google.com/presentation/d/1qS52O0mpflDksKxPuqO-x-rAsMIbnguqluIl1_SwmQY/edit?usp=sharing

Atlantic

• Michael Shirts (chat): One question: what about loading PDB's from AlphaFold2/3 or other protein folding codes? Many people are now getting their initial protein structure to start simulations.

  • JW – PDBs are a giant mess and no one follows residue or atom naming. We’re creating a database of how things “should” work (based on Chemical Components Dictionary). That’s gen1.

  • Gen2 will actually be useful, because we know no one follows these conventions. We will support databases with synonyms.

  • I haven’t looked closely at AlphaFold outputs, but we will be able to publish a synonyms database to support these

  • MS – I have a student who might be able to help compile this kind of information

  • JW – see slide 4 for an explanation of how the workflow will work

• MS – Less big question (can give long answer offline later): how difficult would it be to run Evaluator for optimizations on the national computing resource GPUs?

  • JW – short answer is “it’s in progress, it’s just really hard.” Let’s talk more later.

Science Updates

JW

https://docs.google.com/presentation/d/17_mL6JtLmuixLIHxcZcXNbLd8Xk0oz8cM1UzMjtq9uU/edit?usp=sharing

Atlantic

• JE – if you have technical questions, we will see if Chapin or Jen can answer them.

• JClark introduction

• DC (chat) – Is Antonia Mey also involved with TMFF? She’s been interested in a dataset for a while I think

• Tony’s student Jasmin Guven is giving a presentation in a couple of hours on related topics: https://us06web.zoom.us/j/84603858173?pwd=l9b8Gyp6ja3aBpbtKaRmye4eU0AbUx.1

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In-person meeting plans

JE

https://openforcefield.atlassian.net/wiki/x/BYAcxg

Atlantic

• DC – Haven’t progressed smee work since JH left in Oct, but can present his final work.

• MS – Should build in flexibility in case things overrun

• (DM + JE will figure out how to get an openFE benchmarking update on the schedule)

Q&A

• MT – External folks have been hearing for a long time that we’ve been making a protein FF, graph charges, etc. What is the channel where they should be looking for updates on this?

  • MS – I should be working on a paper on graph charges, currently in brainstorming phase.

  • DM – Graph charges are available, more info coming in preprint. I summarize protein FF as “more difficult than expected, we’re not going to release something until it’s better. We are working to make the amber port more functional”

  • CC – We’ve been working on the livecoms article on benchmarking protein FFs.

  • JE – We probably want to have these answers posted somewhere publicly available. This is why I want us to spend some time focusing on our communications strategy at in-person meeting. Would a blog post in the meantime be a good place for this info?

    • MT – That’d be better than the current situation, but would still leave room for improvement. But would prefer that we have a single-stop answer for outside folks to understand our progress and timelines. Also, would love something that is updated somewhat frequently, since our communication artifacts are frequently just point-in-time. So maybe something tied in with iteration planning or ad board updates.

    • MS – This is a good discussion. Preprints are kinda an infrequent way to give throrough updaes, but would be good to have something more frequent and actionable.

    • JW – Maybe we could get the zenhub roadmap publicly visible once we get it to be correct+updated regularly.

• DD – Any use of alchemiscale that OpenFF is needing in the next few months? We have an agreement to support OpenFF usage.

  • JW – No update at this time, lots of science team turnover.

  • CC – I’ll reach out once we have a protein FF candidate to figure out next steps.

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