2024-02-28 Thompson/Wagner Check-in meeting notes

General updates

• JW –

  • Protein prep workshop went quite well. May be helpful to have you for the 7 AM april series of workshops as well

    • MT – Soft yes but let’s revisit closer to then.

  • Any update on thoughts about attending scipy? Fine if none, just want to reserve a tutorial TA slot for you if you’re coming.

    • MT – I’ll keep thinking about it.

    • JW – Could wait to see whether we get the tutorial accepted and if we have free admission.

  • Syncing up on methane thing

    • MT – I’m impressed with the way that this is being handled by DM, LW, WW. I haven’t had any direct messages/other non-public comms about this, so I’m seeing the same stuff as you. Still undusre about root cause. The water bond length thing was good to fix but didn’t seem related. The number of waters thing is confusing… My top suspect if that this is something to do with how GROMACS minimizes systems. IF someone was going to spend more time on this (which I’m not planning) then the thing I’d look at is comparing GROMACS' minimizer compared to MD at 0 temperature. Maybe something going on with SHAKE/SETTLE here.

  • Nice work handling literally everything while JM and I have been doing comms things for yet another week.

    • MT – Yeah, I look forward to you guys coming back. I worked on the docs failures and didn’t make a ton of progress.

  • A pharma company asked whether the BCCs in Openff-recharge are correct/validated. You’re the current maintainer and I’m nearly certain you have no opinion, but just checkin

    • MT – I haven’t modified them. Ithink they’re >90% correct and some discrepancies were traced to be OE bugs. SB documented a lot of what he did so there are comments and other sorts of into about these. So not a hard yes,but certainly not a hard no.

  • JW – A user at the protein prep workshop asked if we could support silicon conda package deployments. Do you know if we can?

    • MT – DGL is the current blocker. Hopefully will be resolved in the next year. I’ll keep an eye on it and bring this up when it seems ready.

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Trello

Tutorial review

Project Plan: Common workflow conversion via Interchange