Individual updates | DN Started working on deadlines for different projects. Using a tool/technqiue called “critical path”, which will indicate our biggest project liabilities. One thing I’ll need to know is how much time each item will take to be developed. This will be tricky since there’s a lot of unknowns in our processes. In my previous roles this had been a bit easier since I know how long building woudl take to build, how long to hire, etc. But this will be different since it’s a science/technology project. So one thing I want to ask is whether we have deadlines for items and which calendar we follow. JW – Pharma renewals are in october, that could be interpreted as our “year end”. But mostly we’ve worked without deadlines, and just used target dates for FFs to justify priorities.
MT: Bespokefit single installers done (RDKit+AT+xTB) Interchange now has feature parity with the toolkit’s OpenMM export except for GBSA and custom plugins (both pushed to releases after 0.11.0/0.2.0). Need to re-run regression tests but will likely call a meeting soon to give an update to stakeholders. Re-ran value propagation, multi-molecule, and WBO tests, all passing. Single-molecule tests running now, will update on results in a couple of days.
We should drop openmmforcefields from toolkit examples, common cause of breakages/incompatibilities and not a project we have control over. JW – I don’t think we’ll use espaloma in production code. Will instead use nagl+gnn-charge-models. I made a parameterhandler for expaloma in smirnoff_plugins but that’s more of a proof of concept. For openmmforcefields I think we should remove it from our “first class” examples, and maybe keep it just a step above”deprecated”. SB is migrating the repos he’s comfortable with migrating to the openforcefield org, and encouraging us to fork the others when we need to further develop them.
DN – Thanks for looking ahead to potential issues and being proactive in problems that affect the whole ecosystem. I’m really happy that people on this team are motivated to solve our big problems.
DD PB: Last two weeks Worked on Sage manuscript, getting close to first draft but still seems far away. Wrote blogpost on qca-pipeline, sent to David for review. JW – It’s fine for blog posts to have mistakes and typos, so don’t stress too much about it PB – No rush on reviewing, DD.
Getting back to fitting experiments and pushing towards a point release, I have most of the iterations before, documenting them properly and decoupling a mix of improvements:
Valence parameter improvements (Sage) Made a list of missing chemistries (6 parameters), which may not be super relevant, so current solution is to include them in some of the general parameters by making changes such as making a single bond to be flexible or adding an extra valence, we already have and not bother about them much. There are molecules with those chemistries on pubchem though.
JW Bespokefit cleanup+release (Thanks MT for hardening and SFIs!)+support DD – Is xTB as good/equivalent to psi4? JW – We’re not sure, JH suspects that it is but we haven’t tested yet. The quickstart guide now uses xTB for technical reasons, but I added a disclaimer that it’s not the same was what we’ve shown in earlier results.
Prepared to put cross-repo examples into openff-docs (JM will lead this charge, will ultimately include examples like “make parameters with bespokefit, prepare protein using PDBFixer, combine systems in interchange, run calcs using OpenFE software”) User support, specifically pfizer. Tracked it down to a weird OE license issue, redirected to support@OE Mostly clearing backlog of comms, org stuff, PRs This week I'll be charting the path forward for the 0.11.0 release
|