openff-interchange

openff-interchange copied to clipboard

### Description ### Checklist - [ ] Add tests - [ ] Lint - [ ] Update docstrings

mattwthompson

[pre-commit.ci] pre-commit autoupdate

1

updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.2 → v0.4.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.2...v0.4.3) - [github.com/igorshubovych/markdownlint-cli: v0.39.0 → v0.40.0](https://github.com/igorshubovych/markdownlint-cli/compare/v0.39.0...v0.40.0)

pre-commit-ci[bot]

Interchange.to_gromacs() creates a topology with far too many atomtypes, which influences GROMACS performance

4

**Description** When dumping the interchange to GROMACS format, too many atom types are created. This is completely fine in terms of compatibility with GROMACS, but it is causing huge memory...

pbuslaev

Set vdW parameters on virtual sites

1

### Description Provide a brief description of the PR's purpose here. ### Checklist - [ ] Add tests - [ ] Lint - [ ] Update docstrings

mattwthompson

`experimental/openmmforcefields/gaff.ipynb` is failing on openff-docs

3

The `experimental/openmmforcefields/gaff.ipynb` notebook has been failing on openff-docs since the release of 0.3.26. Here's the error: ```python nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ imported.visualize() ------------------ ---------------------------------------------------------------------------...

Yoshanuikabundi

**Description** `ElectrostaticsHandler.charges` or similar dictionaries are ordered but probably just by the order it's created, which is probably just by chance how particles are returned by some iterator(s). It's worth...

mattwthompson

**Description** ```python In [17]: out = ForceField("openff-2.1.0.offxml").create_interchange( ...: Molecule.from_smiles("CCO").to_topology() ...: ) ``` Indexing into a collection to get (physics) parameters with known atom indices requires creating a new instance of...

mattwthompson

**Description** Interchange chooses to have a `.topology` attribute dangling off of it. For better or worse, these have some attributes in common and they can fall out of sync. For...

mattwthompson

[DNM]: Add experimental "auto" idivf

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### Description Requires installing a branch of the same name from the toolkit. Here's a script that demonstrates it: ```python import openmm from openff.toolkit import ForceField, Molecule, Quantity, unit from...

mattwthompson

Improve GROMACS parsing

1

### Description ### Checklist - [ ] Add tests - [ ] Lint - [ ] Update docstrings

mattwthompson