2021-11-15 Core Developers meeting notes

General updates

• JW – Be aware that Thanksgiving is next week – Most US based employees will be off Thursday and Friday.

• MT – I’ll be taking the rest of my vacation for the year and will be unavailable for a lot of December

• JW – Same, people should check the calendar if they need me after Dec 15

• DD – Same

• CC

  • Working on following up with stragglers on LiveCOMS review

  • Tried to submit dipeptide dataset on QCFractal on Fri, botched my conda environment, I think I’ve got it fixed so I’ll try again this afternoon

  • Working on getting library charges for protonation states of amino acids. Having trouble with OpenEye. It’s probably from confs that have hbonds on carboxylic acid groups of side chains.

    • JW – Ran into the same thing last week with bespokefit. I’d like to have a way to make it fall back to a nicer behavior if all the carboxylic acid confs are bad.

    • CC – Yeah, I’m trying to think of a manual fix or some other way to handle this.

    • LW – I used rdkit when I did this and didn’t have a problem. I basically used Simon’s ELF code in the toolkit for this.

    • JW – I’ll keep thinking about a general solution for this – Will contact you if I have a fix.

• MT

  • General PR wrangling

    • Non-biopolymer non-ParmEd example in toolkit. Found a really odd amber error that causes a memory access error when the number of residues in a prmtop is mis-set.

    • Docs improvements – Users guide, changelog, other fixes.

    • Upstream beta/RC tests. Testing against OpenEye and OpenMM RCs. Already caught an upcoming breaking change OpenMM.

    • Bringing units package to to parity with Evaluator units. Some edge cases, eg OpenMM and SI disagree on what a “dalton” is. Polished and made a new release.

  • Feedback from protein-ligand example. Mostly requests for improvements in system building experience. Think we’ll need Topology.from_pdb to load multi-protein and water files.

  • MolSSI MMIC proposal. MolSSI recommended that we take the importers and exporters out of interchange and make them MMIC components. I declined this offer.

    • CC – Could you provide details?

    • MT – The project isn’t well adopted and doesn’t have a clear path forward. Getting this tied in with an uncertain effort would be a huge liability for us.

    • JW – Agree. QCFractal appears to be moving forward despite MolSSI, not because of it. I’m worried that MMIC would go the same way.

    • DD – Agree that it’s a big liability to tie ourselves in with something that’s externally developed. If they gain more adoption in the future we can always revisit this.

  • Started moving stack to M1-compatible builds. Released mdtraj with M1 fixes. We’re still waiting on AmberTools and its dependency chain (parmed is done, packmol seems unmaintained, netcdf-fortran is messy). None of this is super blocking – Rosetta can emulate support for existing packages.

• DD

  • QCArchive

    • changes in openff-qcsubmit in to support Chapin's dipeptide work

    • updating prod envs today

    • scheduled time with Willa on Wednesday to get set up with QCFractal

    • error cycling fix for basic dataset, but error cycling now broken again. Will work on this shortly.

    • submitted two datasets from Pavan in support of SPICE

      • reviewing remaining submissions from Pavan today

  • Protein-Ligand Benchmarks

    • began process for obtaining cloud compute, recognize value to OpenFF of utilizing John's resources for development pathway

    • meeting with him today to discuss what's needed to get resources from AWS programs

      • utilizing Covid as the conduit for funding there

      • might take a while for OpenFF/OMSF to secure its own resource streams here

    • DD – Shared infrastructure for hosting work server and storage - Could be big synergies by sharing with JChodera

    • JW – I can bring this us in project planning and get budget approved.

    • DD – Already discussing this in #foldingathome

    • SB – DHahn may be able to help with cost/file size estimate. Could you share the rough numbers once we start estimating?

    • DD – It can vary widely. I’ll also ask John about the costs of his existing F@H infrastructure on #foldingathome

  • Partner Benchmark

    • shipped retrospective survey; have feedback from 3 partners

    • Lorenzo is now spearheading benchmarking, and will lead Season 2 when it happens;
      transitioned regular meeting to every 2 weeks, pair-meeting with him on the off-weeks

    • all partners except BRI have delivered Sage results for manuscript

• LW

  • Worked through nonbonded issues and debugged my dataset with Simon; Simon has updated nonbonded.

    • Had to debug dataset, some enthalpies of mixing were really pure properties.

  • The entire week spent trying to work directly with evaluator and ForceBalance, as pinning openmm=7.5.1 is not friendly to updated packages

  • Evaluator seems to hang after a few (~3?) hours (no update of progress logs; no increase in file sizes; top shows Python processes with <20% or <10% CPU usage; ps aux shows some generic multiprocessing processes). Stopped at iteration 0 of FB, if properties have been computed, I haven’t found where the output is saved. Tried pushing a few switches, which did not seem to really help:

    • Using DaskLocalBackend (which worked fine for training a force field to 1 property for 15 iterations), with varying numbers of G/CPUs requested

    • Using DaskSlurmBackend, with varying numbers of processes requested

    • Tend to quit jobs after ~24 hours of apparent no progress, so burning a lot of Mobley $

  • PsiRESP 0.2 is pip installable ( ), although RDKit and Psi4 are not. It’s been refactored to use the MolSSI QC stack. Waiting to see if/when QCFractal will patch the issues I’ve raised so I can release 0.2.1 without my own patches – will procrastinate conda recipe until then. Calculates RESP and RESP2 charges

  • Previously: CZI meeting very interesting, lots of tips on managing a research project and on being good science citizens (mostly focused on community building). GSOC 2022 will be very different from previous; no longer limited to students but to all new contributors, longer time frame for more flexible hours

• PB

  • Submitted the openmm datasets, took longer than expected.

  • Some follow up work related to wbo.

  • Tried looking into torsionnet, they released scripts to train a neural net but not the trained model.

• JW –

  • Worked with Danielle Bergazin on bespoke fitting for polymer hosts

  • Started some work on speeding up biopolymer refactor.

  • Mostly tech support