Jeff Wagner

_Repost of https://github.com/openforcefield/openforcefield/pull/432/files#r331088966_ I haven't verified this directly (by making a new repo using the cookiecutter), but will update this Issue when I do so. Basically, I removed our old...

I'm trying to make a new repo where the _repo_ name has hyphens, but not the module name. This is raising the following error: ``` (openforcefield) jwagner@MBP-S$ cookiecutter gh:molssi/cookiecutter-cms You've...

Quality-of-life improvements for hosts of QCFractal manager instances

4

**Is your feature request related to a problem? Please describe.** QCFractal managers work well on a technical level, but it's tough to keep tabs on whether I've set the max...

Externally-made TIP4P-EW box is unstable

3

We're working on implementing virtual site support in OpenFF, but we're finding that, when we use a test case of a TIP4P-EW water box (2100 waters), the simulation coming from...

Standard release process

15

### 1: Get approval from Jeff Wagner (or current [product owner](https://github.com/openforcefield/status)) to release main "as is" ### 2: Create a new release on GitHub, following this template: https://github.com/openforcefield/openff-toolkit/releases/new #### Tag...

Lighter-weight OpenMM dependency and future conda-forge compatibility?

3

To improve ease of packaging and reduce dependency size, it would be good to use a minimal build of OpenMM. This build would just be used to produce openMM-format systems...

Example for putting a ligand into a box of water and equilibrating it

9

@slochower shared the following script with me, which seems to touch on some very useful areas. We should polish in into a full-fledged example! Some complications toward making this into...

Proton transfer in antechamber AM1 partial charge calculation

19

**Describe the bug** _originally posted by Bill Swope_ > Alberto and I have been looking at dipole moments for our neutral benchmark molecules and have discovered several issues that we...

PDBs written using OpenEyeToolkitWrapper don't contain atom names from OFFMol

2

**Describe the bug** ``` from openforcefield.topology import Molecule from openforcefield.utils.toolkits import RDKitToolkitWrapper, OpenEyeToolkitWrapper mol = Molecule.from_smiles('CCO') mol.generate_unique_atom_names() mol.to_file('test_oetkw.pdb', file_format='pdb', toolkit_registry=OpenEyeToolkitWrapper()) ``` yields a pdb file without unique atom names ```...

Spec for undefined stereochemistry

16

## Purpose Because it's a complicated topic, and to maintain the ability to restart this discussion in the future, I think it's important to record our design decisions with regard...