search

openmm / openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.
1.5k stars 525 forks source link

NonbondedForce parameter offsets: Negative scale factors should be allowed #3319

Closed jchodera closed 2 years ago

jchodera commented 2 years ago

3286 added a number of helpful checks for valid parameter values, but it also appears to have restricted sigmaScale and epsilonScale NonbondedForce parameter offset scaling factors to be nonnegative. This does not appear to be necessary, since it should be perfectly reasonable to reduce the initial parameter values (provided the final value doesn't end up negative, but this cannot be checked ahead of time). We in fact use this in perses, since this is necessary for relative alchemical free energy calculations. (cc https://github.com/choderalab/perses/issues/890).

peastman commented 2 years ago

Good catch. I'll fix that.