2024-09-03 BW/LW Check-in

General updates and discussion on projects

• Torsion fitting

  • Restrained minimization

    • Look into as an alternative for constrained minimization

    • Might need to experiment with force constants – work out right force constant to get the desired behaviour

    • Eventually look into working into FB if it works really well

    • Things to look out for – RMSD to the QM structures not too high, the torsion angle itself not veering 5 degrees from the grid point.

    • ForceBalance currently does the following:

      • constrains dihedral

      • Sets 1 kcal/mol/AA restraint on the rest of the atoms

    • We could look into

      • restraining dihedral

      • Possibly setting a higher restraint on the rest of atoms if RMSD is too high in minimization?

  • Next steps

    • Benchmarking current constraint protocol (0 mass thing)

      • RMSD of the molecule at each grid point to QM

        • might be script that does this already in torsion repo

    • Investigating the restraint protocol

      • RMSD of the molecule at each grid point to QM, with different force constants to see which gives best behaviour (high enough that torsions don’t deviate more than 5 degrees from grid points, and RMSD doesn’t deivate “too much” from original QM)

      • FC low enough (hopefully?) that super high forces can relax a little

      • Might need two, one for dihedral, one for the same kind of restraint as ForceBalance uses for other positions

    • Have a look this week

• benchmarking infrastructure repo?

  • progression going

  • Next week will try to set up bigger runners

• smee

  • XFF re-fit. 250k records. 350 steps in 12 days. Using 140+ GB RAM

    • Looking into JHorton’s batching solution

  • Benchmark at 350 steps?

• datasets

  • lipids

    • ball is in Julianne’s court

  • sulfur

    • Fixed bugs, have server running

• chemical perception work – re-fitting force fields

  • Still running

  • TG sent another force field

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• Genentech

  • https://docs.google.com/document/d/1ZJmV9C1IwfRf0UVz6b8Mr_6DvKsQIgfvLhJAScY8K9E/edit#heading=h.97uz1di14ngk

  • https://pubs.acs.org/doi/10.1021/acs.jcim.0c01041

  • https://pubs.acs.org/doi/10.1021/acs.jctc.9b00239

  • LW ping Richard to add to Genentech meeting

• ACS Oct 23rd: tentatively accepted?

Roadmap progress