Dominic Rufa

`openmm-ml` compatibility for generic `MultiStateSampler` objects

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## Description implement compatibility for [openmm-ml](https://github.com/openmm/openmm-ml) (and openmm 8/beta) to allow for generic `MultiStateSampler` free energy/sampling calculations. ## Todos - [ ] Implement feature / fix bug - [ ]...

## Description subclass of `PeriodicNonequilibriumIntegrator` except equilibrium caching is used to maintain equilibrium MD at endstates ## Status - Ready to go

https://github.com/choderalab/openmmtools/blob/7a9c61cea5c657e333f433dabbd7c87624f8227f/openmmtools/testsystems.py#L2334-L2337. i think the appropriate calculation of box length should be ``` volume = (nparticles * sigma**3 / density) length = (volume.value_in_unit_system(unit.md_unit_system))**(1./3.) * unit.nanometers ```

I think it might be useful to fix the indexing of sampled/unsampled endstates. at present, the `multistateanalyzer` will fail if there is only 1 unsampled endstate since it assumes there...

can we incorporate reaction-field hybrid factory into `perses`?

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Can we incorporate [this reaction field hybrid system factory](https://github.com/dominicrufa/aludel/blob/7d5e348a9b5a6b7dd01b85bb3c35c064777f4d80/aludel/atm.py#L756) into the full perses stack? it is not too crappy in comparison to the current vanilla factory at the moment: (vanilla...

Can't run steps of dynamics with NNPOps `TorchForce`

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In attempting to run MD on a `TorchForce`-equipped `System` (the `TorchForce` has the `NNPOps` symmetry functions equipped as described [here](https://github.com/openmm/NNPOps/tree/master/pytorch#example) ), I am observing strange behavior. Namely, I am able...

integrator timing data for tip3p:ligand and protein:ligand simulations suggests a non-pytorch bottleneck?

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 while profiling some protein:ligand and solvated ligand simulation times with `NNPOPS` and `openmm-torch` (treating the ligand with an ANI2x `TorchForce`) I noticed that there is a similar slowdown factor...

`TorchForce` missing `getNumGlobalParameters()` method

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I noticed that while the `TorchForce` supports `addGlobalParameter`, it doesn't have `getNumGlobalParameters` or `getGlobalParameterName`. Is it possible these could be added? or is there a way to wrap this `TorchForce`...