Irfan Alibay

Remove openmmforcefields 13 gaff test code branches

1

Follow up from #893 Once OpenMMForceFields allows gaff for older versions of OpenMM, or once we decide to drop pre 8.1.2 OpenMM versions (whichever comes sooner).

We need tooling to look at key things in a json output file - for example the error log, or any key results.

Solvate with non-cubic boxes

3

OpenMM now supports non-cubic boxes, we should see if we could pass this as a user input (through SolventComponent?).

Encourage properly setting residue names when building form SDF

3

The `UNK` residue is rather meaningless. Is there a way we could enforce (at the SmallMoleculeComponent) both a warning & some kind of convenience method to override the residue name?

We run rever as part of the release process, only Mike knows the process right now :)

Ahead of the 1.0.1 release of OpenFE we should check that OpenFE works with the `main` of: - Kartograf - openfe_analysis - cinnabar

`from_smirnoff` _without_ `charge_from_molecules` silently assigns all isormophic molecules the same partial charges

2

**Description** User case: I construct an Interchange object from a Topology with two or more ismorphic Molecules with different partial charges. In this case the first Molecule has am1bcc charges...

Packmol interface: can't pack mnsol benchmark inputs with assumed evaluator defaults

5

**Description** I'm trying to test if we can pack mnsol (from the 2.0 sage benchmark) with Interchange. My rough understanding (from the paper and some limited looking at the evaluator...

`_apply_hmr` can silently lead to negative values

3

**Description** Appying HMR has no validation / checks in place to avoid zero / negative mass setting. Generally I would say this is rare, but I managed to accidentally create...

`charge_from_molecules` silently ignores isomorphic molecules in list, only using the first entry

2

**Description** Passing two isomorphic Molecules with different partial charges to `from_smirnoff`'s `charge_from_molecules` flag will lead to partial charges only being assigned from the first Molecule. **Reproduction** ```python from openff.toolkit import...