2023-09-20 Thompson/Wagner Check-in meeting notes

General updates

• JW – Some preliminary talk of mat sci PIs going for an NSF grant to start a new OMSF project. Would pay us to train+advise their equivalent of a software scientist. Would be around mid-2024 if it happened.

  • MT – A lot will depends on details of what exactly they’re scoping to do, and how much

  • JW – I’ll keep you up to date on this - Right now it’s in the “maybe we’ll write an application” phase so I’ll send materials if ti goes further.

• MT – Update on POSE grant? How does this interact with us? What should we anticipate with new personnel?

  • JW – I have incomplete knowledge since this is basically Karmen’s grant. But it’s broadly meant to support interoperability/sustainability. some things Karmen pitched were hiring someone to get AI-assisted docs (like an expert chatbot), and to fund a second annual meeting that’s more of a hackathon for expert users.

  • MT – Not sure if I understand tangibly what to expect here - Are we hiring someone to work with me on feature dev? How will this help me/make me more productive?

  • JW – KCJ probably has vague plans right now and should/will soon solicit advice on specifics. She probably doesn’t specifically plan to have a person work on OpenFF goals, but she also doesn’t NOT plan on this. This could be the right time for us to reach out.

  • MT – Maybe after the CCPBioSim prep is done.

  • JW – I’ll reach out to KCJ and express our willingness to talk in a month or more

Trello

(Skipped to save time this week)

UK workshop prep

MT – Basically thinking, first day will have DCole giving a longish talk on OpenFF in general. When it turns over to me, I’ll give a preview of “how it works when things are smooth” - Basically say “when you use this infrastructure you want to get a topology and FF, and get a simulation out of it”. Then I’ll break into the smaller things/details. So I want them to be familiar on the first day with topology, forcefields, and molecules. Then I’ll go into Interchange. On the second day I’ll dig into internals of interchange - 30-60 mins - then get into some more advanced topic like nagl or vsites. It seems like the end of the first day won’t be a big point, we’ll just be discussing how people will be able to use OpenFF to interact with what they know. Second day will focus on getting to an interchange. Day 1 will also include some FF history, water models, future FF work, and mention ff14sb in the context of “what can you do right now?”

JW – What should we do on this today/this week?

MT – Could be good to have a protein/PDB complex loading example or two. Especially getting a reasonable set of PDBs that look like realistic input.

JW – Will do the following:

• Start with solvated+ions PDB and load

• Start with explicit Hs PDB in vacuum and load+solvate w ions+simulate

• Start with explciit Hs PDB in vacuum with ligand and load - Point out small molecule error

• Same as above but with unique_molecules, then solvate

• (Add Hs/caps using PDBFixer)

• (Custom substructure, though this is in private API)

• (Protein with multiple unique molecules, like small molecule + lipids)