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Participants

Discussion topics

Item

Notes

General updates

  • SB – Offline beginning and end of Feb.

    • MT – I’ll be working on doing the testing this week and next, so probably won’t need next stage of approvals until two weeks in the future

    • SB – JW, feel free to bump me from approver position if there’s a holdup.

Round table updates

  • SB

    • Mostly working on GCNs. Building up scripts needed to move forward, building up new molecules by hand to cover things that AM1BCC covers … GNChargeModels GH repo under my personal org, should transfer to OpenFF org.

      • JW – This should be good to go whenever you’re ready.

      • SB – I wasn’t sure if we had a policy for what goes under the GitHub org vs. what stays in individual repos.

    • Many of my molecules had trouble converting Toolkit E/Z bond stereo to RDKit local stereo. I’ve opened a new PR to do this more robustly.

      • JW – Same problem with OpenEye?

      • SB – I don’t think so, we can set CIP stereo more directly with OE. This direct setting of E/Z in RDKit is a known shortcoming, mentioned in mailing list.

    • Also hitting size limits with some file storage, both on QCA and in research codebases. For example, I pulled down lots of QCA results, made ESPs from the results, and now I have these files that took a while to make that I’d like to store with my code.

      • JW – Usually I’d reach for GH release assets. Could also consider using amazon storage, but I’m not sure how much the management and costs would scale here

      • SB – Could use Git LFS on a larger scale.

      • DD – Who manages GH subscriptions/payments?

      • MT + JW – Chodera’s credit card

      • DD – Should probably switch this over to OMSF billing.

      • JW – I’m interested to know where git LFS actually lives and how much it costs, will add “do a research cycle” to sprint backlog.

      • SB – Looks like $5/month for 50 GB.

      • DD – Would this solve bandwidth-constraint issue? (are limited checkouts possible?) I had some experience with PLBenchmarks but could use a better understanding.

      • SB – IIRC, there’s some scope for cherrypicking which files come down.

  • DN

    • Learning about finances, thinking about how different people see OMSF’s strategy. Right now I think it will act as a hub for different projects – Right now OpenFE and OpenFF, Interchange could be a spinoff.

      • JW – I don’t think Interchange should be considered as a spinoff - It’s so intertwined with our other infrastructure and science that it wouldn’t make sense for it to have a separate budget or management

      • MT – Largely agree. Right now Interchange is solidly under OpenFF umbrella. In the future, there’s scope for it to become heavily involved in other parts of the comp chem world.

      • DN – Gotcha. I’ve heard people talking as if there are two projects running - OpenFF and OpenFE. But there are really several significant efforts going on, including interchange

        • JW – And bespokefit

      • DN – I’m just reading into the finances, happy to send a summary as I gain a better understanding.

        • JW + SB – We’ve tried to stay separate from finance, since it introduces a lot of additional degrees of freedom. But happy to consult/advise as single events if needed.

  • CC

    • Spent a lot of time on LiveCOMS review. This is a review article on experimental datasets on benchmarking protein FFs, with contributions from a lot of external authors in our field. So I’m revising this to have a consistent voice and tone, and will send the next draft to the coauthors next week. I’ve got a sense of the consensus from this manuscript and looked into the infrastructure requirements to implement them. They all look reasonable, and should largely slot into Evaluator. .

    • I submitted an abstract to submit to the biophysical society meeting in late Feb. I’m putting together a poster on biopolymers in OpenFF, basically “hey! we can handle biopolymers now”, will send out draft by this afternoon and will ask for feedback.

      • Do we have a repo of common figures? I found OpenFF GDrive slides linked from confluence, but the images are fixed size. Do we have any of them in a more scalable format?

      • SB – I have several of my figures in SVG format, will share these with you. In general it would be beneficial to have a central repo of scalable graphics.

      • CC – Where do we have the big “openff workflow” figure original?

      • SB – I’m not sure. Maybe ask KCJ in #internal channel?

      • JW – I’ll also check whether I have an original copy of that drawing.

  • MT

    • Spent most of my effort hacking away at single-molecule regression tests for interchange rollout. Found discrepancies between (0.11.0 rc exported with use_interchange=True) and (0.10.2 stable release) initially. Also tested against (0.11.0 rc exported using use_interchange=False). Found varying numbers of differences for all of these code paths. Then I tried to reproduce and was unable to find any differences between any code paths (except masses, because we had been changing the element packace to one with different masses definitions).

    • Will move on to vsites this week. Big question is whether all the vsite types can go out to AMBER.

      • JW – The AMBER export question has big strategic/research direction implications. Not sure how to start this conversation in project strategy/interchange planning.

      • SB – Agree. This would be really helpful to understand. Since AMBER can do TIP4P and TIP5P I think our big needs may be covered. Our big need would be nitrogens in heteroaromatic rings (like a 5-membered aromatic ring with an N)… Figure 16.1 in the AMBER manual gives me hope that we’ll have support for what we need. I’ve pasted this image on the #core-devs slack channel.

      • MT – I’m way less familiar with AMBER than I am with OpenMM/GROMACS, so this will require some learning from me. I’m optimistic that we can go to AMBER, but I don’t have much confidence without more research.

      • MT – Could use a scientist(s) to consult on this - People mean different things when they say “support vsites” - One interpretation is “everything possible in the SMIRNOFF spec”, another interpretation is “just a few sorts of vsites are actually important to FF accuracy”

      • SB – I kinda think that the whole SMIRNOFF spec is important - Each type has a physical case where they’re physically justified.

  • DD

    • QCArchive

      • cut release 0.22.0 of QCEngine with Lori early last week; on conda-forge

        • incluces pycpuinfo fix

        • Ben and I established this as compatible with QCFractal master

      • signal handling for QCFractal managers also just merged by Ben, release is imminent; can then deploy this to all compute resources and scale back up on PRP and HPC (e.g. Lilac)

      • re-rolled all SPICE sets that had wavefunctions attached; attempted submission with single-points but still takes way too long in Actions automation

        • will attempt to fix this week

        • new PR on QCFractal for optimizing this a bit

        • will make corresponding PR on openff-qcsubmit

      • error cycling looks like it's choking as well due to memory usage from large DES370K set sigh

    • PLBenchmarks

      • Systems architecture doc draft complete for consumption by AWS folks; worked with John for editing

      • worked with Jeff and Diego to spin up project management and working group

        • call is out for joining as a stakeholder on #developers

  • PB

  • JW

Sprint planning

Action items

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Decisions

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