2022-06-22 Mitchell/Wagner Check-in meeting notes

General updates

• JW – Annual meeting slides - Any high points from new docs I should make sure to show off?

  • JM – The ones you have look good, also consider taking from the bespokefit theory guide - That’s a great docs page.

• JW – Did you get blocked from logging in to the support email?

  • JM – Yes

• JM – Topology refactor polishing is done - PR is merged.

• Skunkworks notebook progress?

  • JM – Notebook works, was able to color atoms/bonds/torsions by the parameters they get assigned.

  • JW – Amazing work. You should join the meeting that I’m having with Diego and Lily right after this so we can make a call on whether we want to show this at the annual meeting.

• JW – We’re going to get into a weird place where we don’t want to be using Parmed and OpenMMForceFields in our examples/user recommendations, but our only alternative is ff14sb, which is slow and not intended for production use. This will eventually be solved when Interchange can import from prmtop and gromacs system fles but that won’t be for a long time.

  • JM – It seems like we should either commit to using the ff14sb port or keep parmed and openmmforcefields in the examples.

  • JW – I’m going to keep having MT move the parmed- and openmmforcefield-dependent examples to an external subfolder. But I’m not comfortable with toolkit_showcase being external. So we should make that use the ff14sb port.

    • JM – Agee

  • JW – So I’d like to remove the external dependencies from the toolkit_showcase example, and replace them with ff14sb and interchange. But then it will become nearly identical to the Interchange protein-ligand example. How can we reduce this duplication?

    • JM – The toolkit showcase and interchange exmaple are kinda different, for example for water the showcase uses OpenMM modeller and the other uses packmol.

    • JW – I’ll ask MT to revert the changes to the toolkit showcase in his PR, and let you take care of it. Ideally, it should:

      • Not use Parmed or OpenMMForceFields

      • Use the ff14SB port for the protein

      • Mention that Parmed and OMMFFs examples are available (point to external folder)

      • It’s up to you whether to make this the first “central doc example”, but leave a breadcrumb trail from the OFFTK examples folder if you do.

To dos

1. (high) Topology refactor polishing - details

2. (high) Skunkworks notebook - Force field blending visualization

3. (high) Topology refactor - better errors from PDB loading

4. (high) refactor toolkit showcase to not use ParmEd/OMMFFs

5. (medium) Skunkworks notebook bespokefit integration

6. (medium) Centralized examples (from 2022-04-27 Mitchell/Wagner Check-in meeting notes)

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

7. (medium) Toolkit docs cleanup

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

9. (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…”)

10. (medium) bibtex blocks for website “how to cite” page on http://openforcefield.org

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

2. (low) Check main website for broken links

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