Dominic Rufa

@peastman, I can update the `openmm-ml` test and push the `nnpops` bits tomorrow.

> We need to take inventory of our current tests and see which ones we skip on CI (currently both `@attr('advanced')` and `@skipIf(running_on_github_actions, "Skip advanced test on GH Actions")` >...

let's see. things that would probably be faster with a gpu: - https://github.com/choderalab/perses/blob/a3366c7c1bdf4a8ca85567d48d9dcacf5e75d16d/perses/tests/test_fah.py#L29 - https://github.com/choderalab/perses/blob/a3366c7c1bdf4a8ca85567d48d9dcacf5e75d16d/perses/tests/test_fah.py#L76 - https://github.com/choderalab/perses/blob/a3366c7c1bdf4a8ca85567d48d9dcacf5e75d16d/perses/tests/test_relative.py#L216 - https://github.com/choderalab/perses/blob/a3366c7c1bdf4a8ca85567d48d9dcacf5e75d16d/perses/tests/test_relative_setup.py#L41 - https://github.com/choderalab/perses/blob/a3366c7c1bdf4a8ca85567d48d9dcacf5e75d16d/perses/tests/test_relative_setup.py#L114 - https://github.com/choderalab/perses/blob/a3366c7c1bdf4a8ca85567d48d9dcacf5e75d16d/perses/tests/test_relative_setup.py#L164 the ones that need to be optimized......

@ijpulidos , if we are using [this class](https://github.com/choderalab/perses/blob/2ff4a7bb631a93716b64f2bd11dc68a2864402cd/perses/rjmc/topology_proposal.py#L1918) for the topology proposal, then regardless of whether we are using a pre-determined geometry-based atom map or a openeye-enabled mcss method, the...

yep, that's the problem. it should be agnostic to the annotations on the new/old atom. and as you can see here , it was a TODO to treat it more...

if there is a constraint that is mapped, then i am pretty certain the hybrid system will retain the old constraint. > Create a network.Graph from the mapping, creating edges...

> This will likely be very brittle, since we would have to thread the needle between C-H and C-F bond differences (~0.25A) while being lax enough to tolerate small deviations...

I noticed these, too. Will give these solutions a try and get back. Thanks for the sleuthing.

you're right. I must be running into a different issue downstream. sorry.

correction: it seems that `getNumGlobalParameters` method is missing _after_ the `Force` is added to a `System` object.