Ivy Zhang

Closing this, since we didn't observe that this addressed our sampling problems

CC: @jchodera @ijpulidos @mikemhenry

>Is the sigma term of the lennard-jones potential affected when alchemically modifying sterics? It looks like it is, see: https://github.com/choderalab/openmmtools/blob/main/openmmtools/alchemy.py#L1379-L1380

@ijpulidos also mentioned to me that the energy discrepancy on CPU is not present when using one of the OpenMM nightly dev builds -- Iván, maybe you could provide more...

Update: @ijpulidos and I are still working on debugging the issue described in the original post -- I created a minimal reproducible example, but it seems like the error may...

@peastman : Iván mentions that we should be able to reproduce the issue when creating an env with conda: https://github.com/choderalab/perses/pull/1124#issuecomment-1349064744 and then running my minimal reproducible example (https://github.com/choderalab/perses/pull/1124#issuecomment-1307599051). I haven't...

I will probably write a tutorial for writing a REST system or simulating a protein-protein complex with glycans

My tutorial is not ready yet, but will aim to have a draft ready by next week!

@sef43 : I've opened a [PR ](https://github.com/openmm/openmm-cookbook/pull/17)with my draft of a tutorial for building a REST system in OpenMM (also includes code on how to use OpenMMTools to run a...

To extract trajectories for each thermodynamic state, you'll need to pull out the positions from the checkpoint file using openmmtools. Here is a script from my recent paper that does...