2022-09-07 Mitchell/Wagner Check-in meeting notes

General updates

• JW – Working on followup workshop announcements, will probably bounce a blurb about the bespokefit and PTM workshops off of you soon.

• JW – Worked with Arjun from Vertex on some bespokefit setup stuff.

  • Part of it was messy un-cleaned-up redis processes that went away when he closedall his terminals.

  • But a harder part was conda envs on linux that use psi4 - Previously we found a combination of channel priorities that make things work, but now there are weird dependency resolutions that are yielding broken builds (for example, taking forcebalance 1.9.3 build0 instead of build1, which then pulls in pymbar 4 (api break) instead of the build1 which would have pulled in pymbar 3. MT recommended setting specific channels for specific deps like he did in a recent PR

• Sprint planning

  • (Done)

• JM – Should we make a fragmenting AM1BCC charge engine?

  • JW – We could, but it’s not in the SMIRNOFF spec so we couldn’t put it in the toolkit. It’d fine if you want to put this in a notebook or somewhere like smirnoff_plugins, just try to limit our liability/maintenance burden.

Todos

1. (high) Resolve feedback on BespokeFit PR and make discussed change

2. (medium) Prepare material for Bespokefit workshop (materials from last time)

3. (medium) Update bespokefit to work with Toolkit 0.11.0

4. (medium) Centralized examples (from)

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

5. (medium) Centralized OpenFF “book” docs

6. (medium) Toolkit docs cleanup

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

8. (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…”)

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

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

11. (low) Check main website for broken links

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