2023-11-29 Mitchell/Wagner Check-in meeting notes

Participants

  • @Josh Mitchell

  • @Jeffrey Wagner

Discussion topics

Item

Notes

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Notes

General updates

  • JW – How was this month? Any smoke I should be aware of?

    • JM – Trying to get traction on CZI stuff hard to start, some personal issues too, not a terribly productive month. It’ll be done at the deadline (Dec 5), hard to estimate progress beyond that.

    • JW – Mind if I throw some technical stuff your way this week?

    • JM – That’d be great, could use some small tasks to build momentum.

  • JW – Want to come to to annual meeting in NL?

    • JM – I’ll think about this. Leaning toward yes, but I’ll let you know next week.

  • JM – Workshop ideas

    • We should do a bespokefit workshop, which could be oriented around “hey, look at the SMIRNOFF spec and what it lets us do”

    • Topology.to_pdb (and possibly also from_pdb)

    • Interchange

    • JW – Agree with the first two, maybe could be good to also ensure the workshops focus on types of chemical systems/use cases.

    • JM – Could have one just be a ton of vignettes?

    • JW – Not a bad idea.

    • JM – So could be like, “bespokefit”, “simulate a PDB with topology and interchange”, and “vignette extravaganza”.

    • JW – Not bad. I’d also like to think about what we want to present and how to present it given that people could otherwise just stumble on this material online.

    • JM – The important thing about a live presenter is that they control the flow+pacing of information.

    • JW –

    • JM – When reading, I have a goal that I want to get out of a text, and I can skim. When I listen to a presentation, I trust the presenter to convey a big picture to me and control what I’m paying attention to. Also presenters can be more persuasive/frame arguments to motivate the audience better. Presenters can also answer questions.

    • JW – Could say “here’s an example workflow, it runs easily with our input, we’re going to have you try putting your own input in and our developers are here to help you get this going”

    • JM – People will come with bad inputs or not understand the context.

Trello

 

To dos

  1. (high) CZI full application (due Dec 5)

  2. (high) Review+merge Topology loading cookbook PR

  3. (high) Add NaglToolkitWrapper to OpenFF Toolkit docs

  4. (medium) Propose 3 workshops for Dec-Feb, including topic and format. (JW needs to report to ad board about this in Dec)

  5. (medium) RNA (openmmforcefields) + small mol/lipid (Sage) example (nucleic acid formulations are a hot topic, could get us funding/users)

  6. (medium) Take a swing at getting bond orders into Topology.visualize (and check whether it’s in Molecule.visualize)

    1. Done, see notes at https://trello.com/c/3py84vBg/689-take-a-swing-at-bond-orders-in-topologyvisualize

Action items

Decisions