David Slochower

Pain points were: 1. Running `packmol` on its own and reading the PDB output was not handled directly by the toolkit, leading to using Simon's really nice solvation wrapper that...

7. Trying to do some downstream analysis after having atom names automatically assigned. It would be super handy to be able to select atoms in an OpenFF `Molecule` or `Topology`...

Hi @iwatobipen and thanks for sharing _your_ code, which I've benefited from multiple times. Exactly right, this won't (yet) work with the latest OpenFF toolkit. The next version of `openff-evaluator`...

> Important note: Populating the ParmEd system's improper attribute is not the desired behavior, since that refers to CHARMM's improper format which is quadratic (?) My understanding, after talking about...

> I am confused about how a .frcmod file gets involved here. To add historical context to this and #304 and #302: these are issues I uncovered while working on...

Does this PR address the ability to change the citation prefix for certain sections? (I'm asking here because I don't think this is explicitly mentioned in any of the issues,...

Oh, neat. A quick check of the documentation doesn't pull up anything for "scope." Do you have a super quick/minimal example of how that might work? Then I can try...

Thanks for the MWE. That is helpful. I appreciate it :)

I'm running into this issue as well. As a temporary workaround, I'm casting the value for `NaN` data points out of range (for example, setting the value to `-1` for...

No, this issue is about analyzing only pieces of the total simulation data (for example, say you want to analyze the first half and second half of a trajectory separately)....