Page Comparison

Science Update

JE, LW

https://docs.google.com/presentation/d/1Ap_nmxlOk3byIp_53U2xoOZZphjjFpM194beP8CaauE/edit?usp=sharing

(Atlantic discussion)

Infrastructure Update

JE, JW

https://docs.google.com/presentation/d/1Kk3tlQ6lVvF6NCqd_5lTsoSpO5WmmzvsH4IoCnCIfG8/edit?usp=sharing
(Atlantic Pacific discussion)

• Interchange itp loading

  • JM – grompp can combine itps into one big top (as an intermediate output on the way to tpr).

  • LW – MDAnalysis has an itp loader - but I’d recommend using grompp at least to validate. I think there’s a gromacs python API that could make this straightforward (https://manual.gromacs.org/current/gmxapi/userguide/install.html)

  • JW – We’d thought about using openmm loader as well but we’re skeptical about the value of daisy chaining converters in general.

  • JM – Gromacs preprocessor (grompp) might really help here and avoid us needing to do extra work.

Project Update

JE, DM

• OpenFF has a holiday shutdown the entire week of christmas and new years eve and day (dec 22 - jan 1, inclusive). You must still request PTO, but everything will be auto-approved.

• NAGL roll-out plans

• https://docs.google.com/presentation/u/3/d/1tZJ6SP9Hzsy1CViCdKC1s4B7JZQifRnO89Q-XWEATmg/edit

• Leadership is planning an in-person work week in Irvine, CA the week of February 17th. Staff are encouraged to attend. Collaborators and contributors are welcome to join, but we will not be able to provide any travel support.

(Atlantic Discussion)

• CC – I will try to join after the BPS meeting ends on the 19th

Shouts-outs

JE

• Lexie McIsaac is leaving us for a new opportunity. Today is her last day. We will miss her stellar contributions across the board.

Q&A

DM

(Atlantic)

• CC – do we have a date set for the OMSF symposium?

  • DM – it will either be the day before or the day after the alchemistry meeting

  • JE – That meeting is May 6-8th. The last I heard, Karmen and Zach were considering the 5th but had not made firm plans yet.

(Pacific)

• LW – Jennifer Clark from NIST is joining OpenFF - Start date Dec 9. Will be a member of the science team but largely working on QM dataset stuff and working with external stakeholders.

  • JW – I’ll spin some technical work off to JClark so that she can get a feel for development and how to engage with the infrastructure team.

  • LW – That sounds good, in general onboarding could benefit from having more one-on-one time and technical working sessions.

  • JM – A reminder about the IDE called “Zed”, which allows for collaborative code editing and execution. Also support for LLM plugins.

    • https://zed.dev/

• LW – I’ll keep an eye on NRP compute over the long US holiday weekend and will shut things down if they look funny.

  • JW – Thanks