2024-04-22 Mitchell/Wagner Check-in meeting notes

General updates

• JW – Reminder: I’ll be leading a tech demo at the annual meeting, I’ll ping you for support/material prep help if needed!

Trello

https://trello.com/b/dzvFZnv4/infrastructure

Workshop prep

• JM – NAGL/AM1BCC charges are different from ff14SB charges. What should we do in vignette?

  • JM – My thinking is to leave the plot comparison in and use it as a launching off point to talk about Rosemary. The fact that the charges are different has implications for interactions between sage small mols and amber proteins.

  • JW – What’s the current example?

  • JM – Uses nagl to charge alanine helix.

  • JW – Would it be terrible to do the splice-and-charge approach?

  • JM – Yes, that was previously a whole workshop on it’s own.

  • JW – Gotcha. And the NCAA is red?

  • JM – Yes.

  • JW – Ok, yeah, let’s keep it as is and be really upfront about the caveats.

• Retrospective: https://openforcefield.atlassian.net/wiki/spaces/MEET/pages/2785542152/Event+notes#2024_03_13-Pacific-Vignette-Extravaganza

  • Would be good to have a workflow diagram for the RNA example (anything using unique_molecules is a little confusing for first-timers)

  • JM will try adding a AMBER lipid micelle/bilayer to RNA example (but will bail if it takes more than 1/3rd of the remaining time to the workshop)

  • JM will update to use openff-2.2.0 and ff14sb_0.0.4 in workshops

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