David Slochower

Hi @rehan1988, we can help with the code and also advise you on some guidelines for the calculation, but only you will be able to look at your protein-ligand complex...

Yes, interesting. Agree with both of you. @jaketanderson are you asking specifically for during the simulation phase or the analysis phase?

Great points. I think it would not be too difficult to add progress bars to analysis following what `bespokefit` does (thanks @j-wags) or tqdm. (Would you be up for trying...

@jaketanderson are you still working on this?

Thoughts @jeff231li?

Sounds good. And @jaketanderson, don't forget to add yourself to the README as a contributor.

I wonder how this relates to some of the things labeled "lambda exchange".

This happened while setting up a static restraint when the target was unable to be set because `pytraj` could not read the initial structure. We should check that `targets` are...

That's a good idea. I think some of the `for` loops can probably be avoided, and if not, can be coded in `C` since they're generally just looping through frames...

I encountered this issue as well. I installed `netCDF4` via `pip` and still experienced gradual slowing with the `NetCDFReporter` imported from `mdtraj` but using `parmed.openmm.reporters.NetCDFReporter` worked as expected. I didn't...