Jason Swails

I really hate when "next-gen" makes it into the name of a product. It's an accurate descriptor for like 2 minutes.

> @swails it seems to me that `reorder` should probably be disabled if you have more peaks than solvent residues. There's just no way to guarantee that the same peaks...

> I think the "do you want to calculate energy" part was to allow just reordering of the waters, right? Yes. > Should the behavior here be that the energy...

I don't use either of those commands, so my opinion would probably be a bit arbitrary here. Is anybody actually _using_ these commands in a non-command way (i.e., a deferred...

-1 on this. lyx is where the Amber documentation is, so in the interest of keeping a single version of the documentation around, we should keep it lyx, IMO.

Oh, this was for the developer docs.

The approach that would execute the fastest would be to build a plugin to compute the forces with your external function. There are example plugins, both bundled within OpenMM and...

> I'm sorry if I touched something that I shouldn't but I think I only installed openMM from conda and then run a file created with charmm-gui. Is there something...

> I am intrigued though, I was of the assumption that all python interpreters are "left to right", so this should not "add keys simultaneously" but in the "left to...

From [the code](https://github.com/openmm/openmm/blob/dd80fb3fdcba6a75803f8e68f444a657fe42d4f5/wrappers/python/openmm/app/pdbxfile.py#L99-L111), it seems that the `label_asym_id` and `auth_asym_id` columns are chosen based on which one specifies the "most" different chains. However, the [`auth_asym_id`](https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_atom_site.auth_asym_id.html) column is the one intended...