2023-03-28 Osato/Dotson/Wagner/Mobley chat

Owned by Jeffrey Wagner, created
Last updated: Mar 29, 2023
2 min read

Recording part 1: https://drive.google.com/file/d/1zy8TqW4rV156J4FLrsRrPNOXUoWuCBVW/view?usp=share_link

Recording part 2: https://drive.google.com/file/d/1pd5SmOxc83r8UVi06xF14EZHTesJLEbo/view?usp=share_link

Discussion topics

Notes

Notes

  • DM – MOsato has worked in simulation space for a while. Joining my lab as a new PhD student. One of MO’s first projects will be benchmarking openff-2.1. The established route here will be to run the separated topology stack as a stable pathway for benchmarking, and if the timing lines up she can also run the Alchemiscale stack to unearth any bugs that appear.

  • DD – This sounds great. We could really use folks looking for issues and reporting them back.

  • MO – Excited to have a non-rotation project.

  • JW – And to clarify, nothing runs today - so this is an informational meeting - We don’t have anything running yet. In a coming week, we’ll use this timeslot again to get this stack running on your computer.

  • MO – I’ll go in to the lab tomorrow to work with Hannah and (someone else) to learn how to do septop

  • DM – Right, and we can get you an early version of openff-2.1 to try putting in there.

  • “Board slides” – https://docs.google.com/presentation/d/1RS__FdkPrZKbHMamX5cUb2x197qyHEzxzQulJJj5Wks/edit#slide=id.p

  • (architecture diagram discussion, see recording from roughly the start to t+10 minutes)

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  • DD – Example notebook for making a network: https://github.com/OpenFreeEnergy/ExampleNotebooks/blob/dcfc1fd4ff3bc29b44abc4677bf6afc2444c4663/networks/Preparing AlchemicalNetworks.ipynb

  • MO – For now, separated topologies is a bunch of python scripts, how would that work here? Do we imagine separated topologies getting into this infrastructure?

    • DM – That would be run totally separately. It’s a different protocol.

    • DD – One goal is for developers to be able to implement other protocols…

    • DM – This may be something further down the line, not something in the short term.

  • JW – MO, it may help if you started attending the weekly Alchemiscale meeting prior to this - Does that work with your schedule/do you have the zoom info?

    • MO – I’ll start attending next week.

  • JW – Relationship to other groups - We (JW and DD) can’t demand your time - Feel free to tell us “no” - You’re the best judge of your priorities and DM should be the person who can help you clarify.

    • MO – Ok

  • MO – What should I ask PB for?

    • DM – Ask him for “the force field that is most likely to be the Sage 2.1 release candidate but is available right now”

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Action items

Decisions