General updates | MT – Cancel Friday one-on-one. Also I don’t have any questions/comments for Peter. Improved GROMACS export speed based on working with HBaumann. 20k atom protein previously took hours, now is ~30x faster (a couple seconds per thousand atoms). There may even be more optimizations left, but this is already a big win. Somewhat concerned about performance regressions for small molecule boxes/simple liquids. It’s possible that liquid boxes will be a little slower, but this is against the background of a global speedup that offsets it. Last communication with HB was “I’ll take a look”, earlier today. Could be in a release in the next few days, but would like to wait for Hannah’s feedback. JW – Cool, were the effects all to GROMACS export, or were some speedups general? MT – These specific changes were GROMACS only, but the some of the general approaches should be applicable to other engines when I go to optimize them. MT – I’m meeting with IA and MH next week, will communicate pydantic 2 plans to them again. You’re free to join but I don’t expect you to. MT – Meeting with ZB next week.
JW –
@here We’re pleased to announce a few recent minor releases:
OpenFF QCSubmit 0.52.0, with opt-in caching of retrieved datasets and records
OpenFF NAGL 0.4.0, adding support for lookups tables to be used in conjunction with
OpenFF ForceFields 2024.07.0, including openff-2.2.1-rc1.offxml, featuring
OpenFF Toolkit 0.16.2, with some minor bugfixes
Interchange 0.3.28 with a LAMMPS export bugfix (and an upcoming release may substantially speed up GROMACS protien exports)Possibly related to QC deployment discussion yesterday? Vanilla installs of openff-qcsubmit aren’t resolving to OFFTK 0.16.2, and conda nightly tests are failing on version check (installed 0.16.1 but latest is 0.16.2). I think this is because of the zstandard pin in the feedstock (which was due to an incompatibility between OpenEye and QCF). Bespokefit CI (which should exercise compatibility for this whole stack) is resolving to OFFTK 0.15.2 (old), QCF 0.53 (old), OE 2024.1.1 (latest), and zstandard 0.23 (latest) MT – Would prefer to be presented this info in an issue tracker/async. Appreciate that it can be stressful to push half-baked info in the open but it’d be better to occasionally ask silly things publicly. JW – Ok, I’ll compile thoughts and post for discussion async
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