Page Comparison

Project updates

BW

• Past week

  • FB with torsion restraints instead of constraints. Run has finished, but haven’t had chance to run benchmarks yet. Final objective function is 4x higher than original sage fit, which is around the size it was with the charge caching bug

    • LW: is the objective function the same?

    • BW: I think so. Just slotted in the restraint code.

    • LW: would we expect benchmarks to show any issues?

    • BW: … this is same objective I’m seeing with Trevor’s force fields.

    • BW: planning to use YDS to benchmark.

  • create_basic_dataset fix. Expecting review in a couple days. Should I re-run hessian dataset?

    • LW: sounds good.

  • yammbs regression test. Patched undefined stereochemistry bug on Friday.

  • Submitted BespokeFit PR

• Next week

  • BW: need to filter Industry dataset again. Will benchmark FB ff afterwards

  • Also hoping to kick off new FB fit.

  • BW: out at SERMACS from Wednesday
    

    • (Postponed) Lipid maps dataset of full molecules

Project updates

AMI

• Past week

  • Setting up S data + torsion multiplicity fit to see effect on PO3R groups

  • DDX method testing

    • (general): putting dataset on QCA-DS seems like a good idea to get an idea of % crashes.

  • Analysis of S data fit

• Next week

  • more on DDX datasets

  • Continue torsion multiplicity fit

  • Get across Evaluator fits on HPC3 – LW will share code repo

LW

• Mostly NAGL issues

• Troubleshooting Interchange

• Project plans:

  • Virtual sites: Virtual Sites Phase I

    • Set up meeting to discuss the plan this week and agree?

    • Same time as science team meeting, but day after

• Next week:

  • Refiltering industry dataset

    • BW: crashed over the weekend, restarted now. It ran out of memory (although error message was that it ran out of walltime)

  • Kicked off new besmarts fit.

    • BW: still running

    • BW: not 100% sure what TG has done, he’s reset values as per his chemper meetings. He’s also reset torsion multiplicities and stuff. Not sure which torsions were affected and in what ways.

    • BW: just training the force field to data now.

  • SERMACS

    • More academic than expected

    • Interesting talk about SAPT – there’s a paper where they used SAPT to generate FF parameters for a whole FF (from Sherrill group)

    • Talked to student from Sherrill group about fragmentation work for SAPT

      • One issue in SAPT is how to fragment – they may often do it manually

    • Met Lori Burns!

• Next week

  • Refiltering industry dataset

  • qcsubmit and bespokefit PRs

    • Fix the issue in bespokefit with generating FB inputs, JW said he would cut release on merge

    • Will fix create_basic_dataset

  • lipidmaps dataset

  • test organometallics dataset

    • ~100 molecule

      • def2 basis sets generally pretty good (preferred ECP), most modern and flexible

        • def2-tzvp, or pd / ppd

        • Recommend diffuse functions for charged systems

      • B3LYP probably fine, but LMI is partial to wb97x-? (d is suggested in strategy document)

      • wb97m-v is what LMI used in previous work. Can’t calculate post-scf properties in psi4, e.g. polarizabilities (doesn’t have analytical gradients)

      • try bp86, wb97x-d

      • Does Psi4 handle ECPs automatically?

        • AMI: yes

Project updates

AMI

• Past week

  • Submitted new NAGL2 timing benchmark

    • 7/10 problematic iodine molecules worked first try, 2/3 worked when AMI changed the guess

  • Got Sage 2.2.1 + S data + TM data fit going

    • Step size was too large in previous fit, so didn’t converge. Tried Goldilocksing steps but either objective function didn’t change too much or fit doesn’t converge

  • Worked on getting useful code onto GitHub/updated on GitHub

  • YAMMBS analysis

    • Found some molecules had large changes in ddE. ~200 mols minimized to slightly different structure, seemed within regular variation. Those had different RMSD and TFD too, corresponding to different geometries.

    • Another group of mols had large ddEs differences, 10-20, where MM structures were basically identical but the ddE changed a lot. This may have been due to the minimum conformer changing

• Next week

  • Benchmarking Sage 2.2.1 + S data + TM data

  • Continue getting code on GitHub

  • Read through VDW fit code/start VDW fit?

  • Maybe resubmit hessian datasets if QCSubmit PR goes through

  • Schedule NAGL2 meeting this week

LW

• Past week:

  • Porting checkmol to SMARTS

  • NAGL release issues and substructure tooling

  • Getting Evaluator working on Kubernetes a bit

  • Agile experiment

• Next week:

  • Work out checkmol licensing issues

  • Working on Kubernetes Evaluator

  • NAGL release

  • Validating Interchange packing and simulation