2024-04-12 OpenFF/FE collab

last week’s notes

2024-04-03 OpenFF/FE collab

solvent padding

• openff solvent padding definition is different to openmm/openfe

  • openff has more padding added for a given stated padding value (padding distance + a little bit of ligand size)

  • all values are above cutoff, so this is an inefficiency rather than a scientific concern

• will raise as something to document better in openfe docstrings

cutoffs

• nb switching function in openfe code path looks different

  • openfe has distance=-1, useSwitchingFunction=0

  • openff has distance=0.9, useSwitchingFunction=1 (presumably on)

  • action: associated issues raised in openfe repo by MT

• nb cutoff seems to get set to 1.0 (with no switching)

  • should be switching at 0.8 to real cutoff at 0.9

  • this is probably scientifically fine, but is another inefficiency

  • action: issue to get raised in skunkworks?

  • put a print statement somewhere on the OpenFF → OpenFE passoff to see if the 10.0 A cutoff is set by OpenFF (right out of Interchange) or OpenFE code (maybe a consequence of some FE setting being applied after)
    
    

ongoing work

• chosen this as test molecule: COC(=O)c1ccccc1

• RG running back to back AFEs of this

• MT still writing comparison codes

• MT wrote code path for non-water solvation via packmol/interchange