2025-09-24 All-hands meeting

Science Updates

LW

https://docs.google.com/presentation/u/0/d/1f9bczwHVsqcz8PlIXvDcxi67MtnSr3jSIBhE8aoyj48/edit

https://youtu.be/y-GsvFOwP3A

• DC – I’m giving a workshop in ~3 weeks. Should I use AshGC as shown here?

• JW – Yes, we will likely have rc2 available at that point, but not a full release. But the default versions of toolkit, etc will be NAGL-compatible, so I think this should work well.

• DC – Results from splitting N parameters?

  • MT – will share results when I have them!

• JW – this recording was from last Wednesday, then Chapin gave another presentation on Thursday. Do I recall correctly that he identified Null 4-mer-AAQAA3 as the most promising?

  • LW – He had not completed tier 2 benchmarks by then

• JM – At biopolymer ff meetings, I always wonder if we are trying to make torsions impose hydrogen bonds. Why don’t we put in explicit H-bonds?

  • LW – CMAPs might be a more productive next step. But it works for Amber

  • JM – it feels strange that we are trying to reproduce a non-bonded phenomenon with a bonded term.

  • LW – Chapin’s original project plan never contemplated that it would take this long to reproduce the success of the Amber force fields

  • JW – I wonder if a virtual site would help model H-bonds

  • JE – Ron Raines studies Polyproline helices stabilized by N -pi* interactions, and his talks will make you question using MM to model proteins. https://pubs.acs.org/doi/10.1021/acs.orglett.6b01655

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Infrastructure Updates

JW

https://docs.google.com/presentation/d/1SOq6qwDJoJhOj_uAQ_5MuKwl1xpx8Oefs6DwU5UNs3M/edit?slide=id.g22ab2c250b6_0_13#slide=id.g22ab2c250b6_0_13

https://youtu.be/8Zf-jIe2GaQ

• JM – What happened to hashes on the NAGL tag?

  • JW – they’re optional

  • JM – will we have a policy of including hashes in our releases?

  • LW – yes.

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Communications micro-workshop

JE

https://docs.google.com/presentation/d/15IQgmB4Dz9QDdFnq9LvVMD5NVjlZWJVSLULcEmHjX3Q/edit?usp=sharing

https://projects.iq.harvard.edu/files/hks-communications-program/files/how_to_write_an_exex_summ_to_use_4_18_18.pdf

https://docs.google.com/document/d/1V0NiF7GCNosfM4H6aIx0RnfrfUCu-fWkWWmEiX69OvE/edit?usp=sharing

https://docs.google.com/document/d/1cuPTdVN_BRqYdbgD76OK1JUIjJgef4YPgSDkA2i7I7M/edit?usp=sharing

Shouts-outs

JE

Lily’s shouts-outs:

• shout outs to everyone involved in back to school week month, it was fantastic seeing everyone put their own twist in their projects and the results will be valuable and exciting. Special shout out to Jen and Josh for going out of their way to improve processes where they could — I always learned something new every time I reviewed one of Josh’s PR. Special shout out also to Matt and Jeff for also somehow juggling back to school month with pontibus and normal infrastructure fires, that was super impressive!

  • JW – Seconded, big shout out to Matt and Irfan for all the work and diligence on the pontibus work.

• Also this should have gone out last month but huge kudos to Jeff and Matt for all the work it took to make NAGLCharges happen!!! There was a lot of coordination across many different repos and a lot of technical questions to solve.

• Shout out to Chapin for the new format he’s using for the biopolymers meeting, the last meeting ran impressively smoothly. Also huge shout out to you (James) for putting the time into holding these workshops and helping us all get better at these fundamental skills!

• Lastly a shout out to Karmen for getting the budget in order, it must have been a tremendous amount of l work but really vital to the organisation and we’re all very appreciative of all the time she put into straightening it out

JC – Shout out to Finlay, since three of our cross-training project were based on his work!

FC – Then I’ll have to shout out Simon Boothroyd and and Josh Horton for writing most of the software I’m using!

JW – I don’t think FC intended for his Descent workflow repo to be shared and used in production, but that’s what we did!

Q&A