2023-09-13 All Hands Meeting

Updates

• JW – Software ecosystem

  • Some messiness with Pydantic v2 release recently, Matt is leading the charge to update our ecosystem.

  • Big breaking QCFractal release happened yesterday:

    • JW is working on fixes for QCSubmit to continue working with the breaking release

  • QCSubmit is no longer broken for working with legacy QCFractal

  • BespokeFit had an upstream dependency incompatibility, that’s been fixed so conda installs should work again.

  • Nagl will soon be available publicly in the openFF toolkit.

  • OpenFF toolkit has prototype support for custom substructure loading - It’s basically a subset of SMARTS but with explicit formal charges and bond orders.

• Fundraising updates (DLM):

  • (New partner not public)

  • Ongoing discussions - brief list - Talking to US Merck, SandboxAQ, Novartis, Biogen, a few others.
    
    

Recognitions

• David Hahn’s paper benchmarking binding FE calcs has gone to preprint and been submitted to JCIM. Glad to see that going out. https://chemrxiv.org/engage/chemrxiv/article-details/64e86ea479853bbd7862b98a

• JE – Open mic for shout-outs - Would love to have folks bring in cool tidbits of progress. Could turn these into social media posts.

• JW – Paul Labute’s work on force field fitting is pretty impressive.

Q&A

• DC: On BespokeFit (relevant for our upcoming training workshops) should we use an all-in-one environment?

  • JW: Yes.

• DM – Really cool xtalpi FF paper that just came out. We’ll probably run something like a journal club when LW is back - Would love to discuss which of their ideas we can apply to our work. Is that this paper? https://chemrxiv.org/engage/chemrxiv/article-details/64e6b390dd1a73847f60f727

• JW – The scale of alchemiscale is truly impressive.

  • DD – up to 500 workers

• LM – What is alchemiscale?

  • DD – It’s a distributed way to run free energy calculations. Allows for stuff to run on a wide variety of compute backends/clusters.

  • Lets us make use of the “table scraps” of academic clusters.

  • Weekly “Alchemiscale” meeting is infrastructure-focused.

  • Currently we can use HPC / Kubernetes clusters.

    • Major push for the fall is to run on F@H

  • Strategic plan is to make evaluating candidates force fields massively parallel

• JE – From OMSF level, we have Julia from Rosetta on OMSF staff now. She led a big benchmarking push for Rosetta to make sure the releases were held to standard measurements. It may be good to get her input on our benchmarking strategy.

  • JC – Is she still at Flatiron?

  • JE – I think she announced she was leaving.

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• JC – Landscape analysis for NIH resubmission - Would love to have eyes on this and make sure we’re not missing any big efforts.

  • https://docs.google.com/spreadsheets/d/1e1nGFvSwu-DL04pzQxf_Ehke4TQ6XAa3yuK-ovo_IkA/edit#gid=0

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Question about QCSubmit

JW, TG, JC, BW

to_basic_result_collection() bug

BW – kwarg driver=hessian

JW is not the only person who finds this confusing.

Ask Chris Iacovella