2024-08-20 BW/LW Check-in

General updates and discussion on projects

• Torsion fitting

  • BW: tried not freezing the atoms, restrained the dihedral by 1000 kJ, positions look the same

  • LW: might be good to pull out the function and check the code is running as expected

  • MS (in Slack):

    • So, another question as I try to get better instincts for this - are these parts of the potential energy surface the right ones to be matching, since the system spends less time in these higher energy configurations?  I realize, of course, that the relaxed portions of the MM energy surface will not be relaxed ones of the QM system . . . I realize, also, that you all have been thinking about this plenty already, in order to make sure the QM and MM are actually being compared at correctly corresponding coordinates, rather than non-corresponding coordinates.

• benchmarking infrastructure repo?

  • bzipping, and dumping QM coordinates, cut database size into a quarter (~50-60 MB)

  • MT: looking into new formats, e.g. JSON

  • BW: can now upload files to Zenodo

  • BW: could use clarification on status and how far along this will be, i.e. when it will be published. Happy to maintain

  • MT/BW meeting: AWS could run this for $10-15

  • Statistics at the end take ~1 hour

• smee

  • BW: keep running out of memory when loading dataset

  • BW: looks like issue is in QCPortal and caching. Otherwise will write data to disk and reload it

  • LW: is batching connected to this? DCole and JHorton found this helped.

  • BW: that’s probably during training, this is during data formatting

  • LW: working with scale factors too

• datasets

  • BW: need to get back to FPickard, MShirts about updates

    • Julienne H might be involved with this

  • LW: another sulfur dataset: Increasing dataset coverage

  • Open

    

  • LW: if we target ~20 molecules per group we can split into training/testing

  • LW: alkanes are nearly done, need to set up new NRP workers

  • LW: genentech might be moving forward soon

• chemical perception work – re-fitting force fields

  • BeSMARTS FF running, on iteration 22. Objective function still pretty high. Running with 2.2.0 priors.

• infrastructure work

  • mostly the benchmarking stuff

• LW: let’s look at the roadmap plan next week