Forrest

To clarify, I meant this issue to be about all of our C++ wrapped code and not specific to the context. We have this issue in a few places and...

Been running this on CDK2, Hif2a, SHP2 from here: https://github.com/MCompChem/fep-benchmark/ So far things are looking pretty good. Takes about 15 seconds per pair at the moment (32 core machine, but...

After some digging the issue with the `test_vacuum` test. The nans come from from this line: https://github.com/proteneer/timemachine/blob/master/slow_tests/test_vacuum_importance_sampling.py#L90 Looks like none of the torsions for the vanilla end up on the...

@maxentile I had seen that and modified it to be `8`, but had thought because I have 24 cores it was an atypical number, not sure how many cores @proteneer...

We now check that the box edge lenght >= cutoff / 2. This check is in the non-bonded potential, though verifying it in the context would be good as well.

Can we close this?

Could you specify how we want this to function? Right now we have the call to configure it to use 64 bit in enough places that I would imagine almost...

Done in https://github.com/proteneer/timemachine/pull/867

Been thinking about this PR a lot recently, seems super useful. One point I had brought up online was that if the initial mapping is generated with different parameters (say...

> @badisa when you get a chance, not sure why this test is failing: > > ``` > tests/test_local_move.py::test_local_md_particle_density[1.0-True] FAILED > > ============================================================================================================================================= FAILURES ============================================================================================================================================== > _____________________________________________________________________________________________________________________________ test_local_md_particle_density[1.0-True] ______________________________________________________________________________________________________________________________ >...