2023-04-26 Mitchell/Wagner Check-in meeting notes

General updates

• JW — RAlford said the docs were great

• JW — OFFTK 0.13 release - Should have everything needed for annual meeting

  • Topology.from_pdb (no stereo guard)

  • Private additional substructures kwarg

  • Private Nagl prototype

• JW – Started https://github.com/openforcefield/2023-workshop-vignettes

• JW — Roadmap update - Seems likely to be approved in a form like this by Gov board - https://docs.google.com/presentation/d/18xuvuVlglCk-cekJ_ZY8auYtrZd61EwI1bkWZJUnlgY/edit#slide=id.p

• JW — Packmol wrapper has been ported to interchange - So we can do mixed solvent boxes

  • JM – Wouldn’t this belong in the Toolkit? Once users have an interchange it’s kinda too late for them to want to pack a box.

  • JW – I don’t really think so… Maybe it’d be best in openff-utilities

• JM – Filed for reimbursement from Remote for the US trip. Looks like it won’t arrive for two months/pay cycles. This is very slow.

  • JW – Wow, that is really slow. Be sure to apply for a ramp card. If you don’t have a ramp card by the meeting, have someone with a card pay for your meals and on-the-ground expended.

• JM – Should I anticipate helping industry speakers clean up their code?

  • JW – RAlford yes, probably not WWu, JBluck, or BSwope (though I’ll tell them to avail themselves of your proofreading if it comes up)

Talk prep

• JW – MT will work to fill out vignette slides starting next Weds - we need to put placeholders showing what we want - He’ll make code to prep system, but we have to run sims and record video ourselves.

• Reviewed slides

• JM and JW will continue working on slides/vignettes/timing and chat again next week.

Trello

Todos

1. (highest, due next Jeff meeting) Outline talk slides (can be just bullet points, just get concepts/timing roughly chunked out)

2. (highest) – Continue outlining talk slides, work out rough timing, start work on some vignettes, figure out nglview → gif pathway

3. (high) Centralized OpenFF “book” docs

4. (high) Centralized examples (from)

   1. (high) bespokefit protein-ligand or ligand-in-water example

5. (medium) Toolkit docs cleanup

6. (medium) Toolkit revised user guide (+-unifying/centralizing package user guides)

7. (medium) Come up with “milestones” for making first of three videos this year (like, “first video on covid spike protein and small molecule, filmed this day, edited in that range, etc…”)

8. (medium) bibtex blocks for website “how to cite” page on

9. (low) Propose policy for using GH citation machinery

10. (low) Check main website for broken links

11. (low) Conda env yamls for each release (automated inside of Toolkit’s single-file-installer action)