Andrea Rizzi

If it is of any help, I've just merged this PR (#1207) that adds support in YAML to read CHARMM psf files so you may go through their setup pipeline...

Hi @shitanshu-cell . If you have set the `logging` level to `DEBUG`, you should see timing information in the log. In case it's useful, there's a utility function in YANK...

You'll have to run the python script with your mpi launcher. This depends on your system, but an example is ``` mpirun -n 4 python myscript.py ```

Hi @Teohoho . That step is done on the CPU. You can switch to GPU it by changing [this line](https://github.com/choderalab/yank/blob/master/Yank/multistate/multistateanalyzer.py#L1698) to use `"CUDA"` or `"OpenCL"` instead, but you may end...

Thanks for the feedback! Those are known problems and we're planning to fix them eventually. > Is there a way I could get it to print out this value, so...

Sounds good. Consider also following the suggestion from @jchodera and start your simulations with `lambda_restraints: [0.0, ...]`. That removes the need for unbiasing completely and the analysis should be much...

We don't have a clear answer to that question yet. Somewhat speculating, as long as the `lambda_restraints` is 1.0 when you start turning off `lambda_sterics` from 1.0 to 0.0, it...

Hi @Byun-jinyoung . Yes, that looks like a leap error. Which leap command and script are you using to try to reproduce the error? Is the leap script you are...

Yes, and I think those examples require a couple of fixes after the last changes to the YAML format. We need to activate automatic testing of those examples.

I don't think we have a specific timeline, but I will progressively try to get to all these issues in the next few months, while we're working on the YANK...