touchpoint_04 Apr 2024

Agenda

1. Housekeeping and review TODO (15 mins)
2. Review project board (30 mins)
3. Plan next week (15 mins)

Attendees

1. Mike
2. Stephen
3. Steven
4. Cameron
5. Amjad

Meeting notes

• Mike is still working on packaging the cod tool. It has several dependencies such as perl modules.
• We did the walk though of the mini mvp example notebook covering packing and force field setting
• Currently the packing is a wrapper to packmol implemented in interchange. This is already a means to reduce the amount of code we need to write for packing boxes. During testing we will check if this does not meet any of our needs (e.g. slabs) and see what needs to be added. We identified a few common use cases:
  • small molecules
    • slab (xstal with given face exposed z, xy pbc, what to "fill" z plane at given density, no fractional mols (if com is inside slab, generate). Packages that do slab generation: pymatgen, atomic simulation env (ase)
    • CSP boxes will include unit cell prep and super cell prep. Inputs will be mol, unit cel parms, symmetry operations etc. For csp, you don't want the xstal to force the mol into a confirmation
  • large molecules
    • prevent overlaps with solvent, large enough box
    • build/pack at low density and shrink to desired density (don't simulate protien during shrink)
• Next we talked about the force field parameterization. Current notebook describes how to apply off-the-shelf force fields. Can we read other force fields, e.g. lammps force field?

Action Items

1. Create a new user story for Bespoke FF integration with OpenFE workflow - Yilin, Kaushik
2. Create slides with roadmap and where we are at - Mike