2022-04-27 Mitchell/Wagner Check-in meeting notes

Owned by Josh Mitchell, created
Last updated: Apr 28, 2022 by Jeffrey Wagner
2 min read

Participants

  • @Jeffrey Wagner

  • @Josh Mitchell

Discussion topics

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Notes

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Notes

General updates

 

  • BSwope – “Bespokefit docs are really top notch”

    • Notes from bespokefit working session:

      • OMP_NUM_THREADS and n_cpus for XTB should be recommended to be 1 (it’s much slower if more CPUs are added thanks for quirks in QCEngine)

      • Made a Swope example - Could be good for docs/example material

openff-bespoke executor run --smiles "CC(=O)NC1=CC=C(C=C1)O" --workflow "default" --output "acetaminophen.json" --output-force-field "acetaminophen.offxml" --n-qc-compute-workers 6 --qc-compute-n-cores 1 --default-qc-spec xtb gfn2xtb none

 

  • JW – Could be neat to turn the above into an example, though it may go slightly beyond the strict scope of bespokefit - It uses OpenMMForceFields' TemplateGenerator to load the bespoke FF, and then OpenMM’s Modeller to add a solvent box. So maybe something in a toolkit/higher-level user example showing how to set up multi-component simulations with bespoke FFs (possible also including a protein?)

  • JM – Could make this an optional section in the toolkit showcase?

    • JW – That’s a good idea. Could have an if statement that defaults to False but that a user could override to do a bespoke fit.

  • JM – The Interchange and OpenFF Toolkit “toolkit showcase” examples are nearly identical

    • JW – I anticipate the Interchange showcase superseding the toolkit one.

    • JM – Maybe we should have centralized examples for stuff that spans repos?

    • JW – That’s a good idea. Could take the following examples from the OFF Toolkit and I won’t ask any questions:

      • swap_amber_parameters (both examples in here)

      • toolkit_showcase (since it will be superseded by toolkit-and-interchange-and-maybe-also-bespokefit showcase)

      • using_smirnoff_in_maber_or_gromacs

      • using_smirnoff_with_amber_protein_force_field

      •  

  • JM – I hooked up http://docs.openforcefield.org . Still need maintainer access to evaluator, recharge, and interchange docs on recharge to get those set up those on readthedocs.

    • (JW asked MT and SB for maintainer access on core-devs)

    • JM will add openforcefield/standards to the landing page as well.

  • JM – I merged my PR but the QCSubmit docs aren’t rebuilding. Not sure why. Maybe RTD is monitoring master but the dev branch is now main? I’ll check again after I get maintainer access.

  •  

 

Todos

  1. (high) QCSubmit users guide (in progress)

  2. (high) Interchange pre-release prep

  3. (medium) Toolkit docs cleanup

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

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

  6. (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…”)

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

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

  9. (low) Check main website for broken links

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

Action items

Decisions