Iván Pulido

Yes, considering benchmarking is becoming bigger we do want to have better (more efficient and friendly) and smarter ways to deal with these situations. I wonder if we want to...

Seems like it is becoming even more beneficial to have a whole module for the benchmarks part of perses https://github.com/choderalab/perses/pull/1050#discussion_r903025368

> Is this for performance benchmarking (ns/day, time for a single calculation) or accuracy benchmarking? This is for accuracy benchmarking. That is, running the systems in the `protein-ligand-benchmark` dataset and...

Directly changing these will break the API compatibility. Considering that this code is still experimental and in a 0.x version that is subject to API breaking changes, I think this...

I computed torsions for the different systems that are output of the scripts that @zhang-ivy shared (5 samples each): * capped aa: doesn't have the issue * small peptide: has...

> @ijpulidos : Great work tracking down the problematic torsion! Can you figure out which atoms those indices correspond to? @zhang-ivy Wouldn't that just be the same indices (plus 1,...

@freeenergylab Currently all of our branches depend on OpenEye. So far, there is not much else other than what has been said in the original linked comment. It is still...

Nice to see @sukritsingh is using perses. Thanks for your feedback! @zhang-ivy Ah! I didn't know this. Thanks for sharing this information. I guess this issue can be used then...

Examples of proteins with terminal caps prepared with Maestro should be really helpful for this purpose.

Use examples from #919