Ivy Zhang

>In that case, you probably want to find the size of the axis aligned bounding box (maxRange-minRange in the code quoted above) @peastman : It's not obvious to me how...

Ah sorry, I think I was misusing some of the terminology since I'm new to thinking about solvent boxes. >Of course, you could try to first rotate the protein before...

I just realized the PDB file I had been using was the output after alignment to a variant of the same protein. When I look at the PDB file without...

> in principle, we can edit solvents.yaml in openmmforcefields so as to generate the combinations of water+ion parameters we need? I'm not familiar with converting the solvent forcefields -- I've...

We discussed at the perses dev sync today that either @ijpulidos or @mikemhenry would chat with @jchodera to discuss how to implement this. The plan is to: 1) Adapt the...

Note from perses dev sync on May 9th: We also want to make d_u/d_lambda available during the simulation.

The particles are already sorted into classes, so step 1 is already done. I'm not sure how to implement 2 and 4, but we can discuss more on Monday. Importantly,...

@peastman Here's a system and state xml that is a typical use case for me (its the RBD:ACE2 complex). Its 185378 atoms. [rbd_ace2_example.zip](https://github.com/openmm/openmm/files/7079777/rbd_ace2_example.zip) Note that the `CustomNonbondedForce` has the long...

Great, thanks for the update!

@peastman Just following up to see if you have another update on this!