sgill2

@khburley Your PR looks good for the most part, except some of your tests are failing. The output makes it seem like the test fails because `getRotBondAtoms()` can't find the...

@nathanmlim This should be ready for review.

I'd say we should cap the relaxation testing at 1000 `nsteps_neq` since updating the lambdas is slow, so anything longer than that would probably be painful to test*. I'd probably...

Hi @luancarvalhomartins, Could you post the scripts/files you used (or a minimal example)? From the traceback you posted it looks like there's a problem with openmm, but I can take...

Since we have to worry about external protocol work (external as in work from outside the lambda perturbations) we can't use the NonequilibriumLangevinIntegrat class directly. I think that there were...

Thanks for the input @pgrinaway! @davidlmobley I haven't brought the integrator into github yet. I'll go about putting up a WIP for it now.

The external work should be zero in the case of a rotation/translation of a given whole fully non-interacting ligand. However, we're also looking to apply other moves, such as rotational...

Upon further discussion we think it might still be relevant to test a metropolized and external protocol approach and see how they perform in different cases. If we consider the...