Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / openforcefield/openff-interchange issues and pull requests

#787 - Internally use vdW section 0.4

Pull Request - State: open - Opened by mattwthompson over 1 year ago - 2 comments

#786 - Internally use `vdWHandler` version 0.4

Issue - State: open - Opened by mattwthompson over 1 year ago

#785 - Allow Pydantic 2 in test environments

Pull Request - State: open - Opened by mattwthompson over 1 year ago - 1 comment

#783 - Support 4-site water models in Amber export

Issue - State: open - Opened by mattwthompson over 1 year ago

#782 - Make OpenMM an optional dependency

Pull Request - State: open - Opened by mattwthompson over 1 year ago - 1 comment

#781 - Support vdWHandler 0.3 and 0.4

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#780 - Use Pydantic v1 API from v2

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 2 comments

#779 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#778 - Update Foyer migration guide and `Interchange.from_foyer`

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#776 - pydantic 1.10.12 breakes

Issue - State: closed - Opened by xiki-tempula over 1 year ago - 3 comments

#775 - Make `Interchange.from_openmm` a class method

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#774 - `Interchange.from_openmm` not tagged as a class method

Issue - State: closed - Opened by mattwthompson over 1 year ago
Labels: bug

#773 - Remove `.mdtop` from docs

Issue - State: closed - Opened by mattwthompson over 1 year ago

#771 - Maintenance updates

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#770 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#769 - Add "how to cite" section

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 2 comments

#768 - Add link to Interchange docs in About section?

Issue - State: closed - Opened by jchodera over 1 year ago - 1 comment

#767 - Gromacs topology files do not keep correct atom type names

Issue - State: closed - Opened by tlfobe over 1 year ago - 5 comments

#766 - Update gromacs.py to pass input edr path in _parse_gmx_energies routine

Pull Request - State: closed - Opened by pbuslaev over 1 year ago - 1 comment

#765 - gromacs._parse_gmx_energy has hard-coded path to out.edr file

Issue - State: closed - Opened by pbuslaev over 1 year ago - 1 comment

#764 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#763 - Refactor OpenMM positions export to common module

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 2 comments

#762 - Reconfigure common objects into fixtures

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#760 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#759 - Clean up internal processing of non-bonded data to OpenMM

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#758 - Use OpenFF Toolkit 0.14.0+

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#757 - Further tidy prose in examples

Issue - State: open - Opened by mattwthompson over 1 year ago

#756 - Central examples

Pull Request - State: closed - Opened by Yoshanuikabundi over 1 year ago - 7 comments

#755 - Use `openff.toolkit._tests`

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#754 - Fix protein_ligand example's call to pack_box

Pull Request - State: closed - Opened by Yoshanuikabundi over 1 year ago - 8 comments

#753 - Support non-rectangular boxes in LAMMPS

Issue - State: open - Opened by Yoshanuikabundi over 1 year ago

#752 - Support non-rectangular boxes in Amber

Issue - State: open - Opened by Yoshanuikabundi over 1 year ago - 2 comments

#751 - Test on Python 3.11

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#750 - Test on Python 3.11

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#749 - Test on Python 3.11

Issue - State: closed - Opened by mattwthompson over 1 year ago

#748 - Do not inherit from `BaseException`

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#747 - Make custom exceptions subclass Exception rather than BaseException

Issue - State: closed - Opened by Dunni3 over 1 year ago - 1 comment

#746 - Fix turning off of switching function in Amber driver

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#745 - Amber driver misapplies switching function

Issue - State: closed - Opened by mattwthompson over 1 year ago
Labels: bug, dependencies

#744 - Remove binder

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#743 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#742 - Make HMR simulations easier

Issue - State: open - Opened by mattwthompson over 1 year ago

#741 - Add JSON roundtrips

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 2 comments

#740 - Update file structure of examples

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#739 - Process Ryckaert-Bellemans torsions in OpenMM driver

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#738 - Switch to `setup-micromamba`

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#737 - Improve GROMACS parsing

Pull Request - State: open - Opened by mattwthompson over 1 year ago - 1 comment

#736 - `get_openmm_energies` ignores `RBTorsionForce`

Issue - State: closed - Opened by mattwthompson over 1 year ago

#735 - Do not perform SHAKE in Amber driver

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#734 - Update toolkit constraint

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#731 - Export non-rectangular boxes to GROMACS

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 8 comments

#730 - describing pi orbitals for rings

Issue - State: open - Opened by peterjohncherry over 1 year ago - 5 comments

#729 - Add support for using customised packmol input file

Issue - State: open - Opened by taidbui over 1 year ago - 2 comments

#728 - Wrap GROMACS atom indices at 100,000

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#727 - Maintenance updates

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#726 - Fix a strange bug with Python 3.9

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 3 comments

#725 - Add `Interchange.to_openmm_simulation`

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 3 comments

#724 - Fix some formatting issues in GROMACS files

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#723 - Small bug in Gromacs output (Sage 2.1.0 only)

Issue - State: closed - Opened by gvigers over 1 year ago - 5 comments
Labels: bug

#722 - Make OpenMM an optional dependency

Issue - State: open - Opened by mattwthompson over 1 year ago - 2 comments

#721 - Ensure `[ settles ]` are written in nanometers

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 2 comments

#720 - `[ settles ]` section written without checking units

Issue - State: closed - Opened by mattwthompson over 1 year ago
Labels: bug

#718 - parmed can not read Amber prmtop files created by interchange

Issue - State: open - Opened by steinbt2 almost 2 years ago - 5 comments

#718 - parmed can not read Amber prmtop files created by interchange

Issue - State: open - Opened by steinbt2 almost 2 years ago - 5 comments

#717 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago - 1 comment

#716 - API and tooling cleanups

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 2 comments

#715 - Add v0.3.3 release notes

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 1 comment

#714 - Update water example

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 2 comments

#714 - Update water example

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 2 comments

#713 - `Interchange.to_openmm_simulation()`

Issue - State: closed - Opened by Yoshanuikabundi almost 2 years ago - 4 comments

#711 - Update auto-generated `sander` input script

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 1 comment

#710 - Amber driver does not appropriately constrain bonds

Issue - State: closed - Opened by mattwthompson almost 2 years ago
Labels: bug

#709 - Optimize execution time of common operations with `Quantity`s

Issue - State: open - Opened by mattwthompson almost 2 years ago
Labels: enhancement

#708 - Update protein-ligand example

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 5 comments

#707 - Packmol improvements

Pull Request - State: closed - Opened by Yoshanuikabundi almost 2 years ago - 18 comments

#706 - Update solvent example

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 3 comments

#706 - Update solvent example

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 3 comments

#705 - Fix setting vdW 1-4 scaling factor in OpenMM export

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 1 comment

#704 - Amber driver reporting incorrect energies if constraints are involved

Issue - State: closed - Opened by mattwthompson almost 2 years ago - 7 comments
Labels: help wanted, feedback needed

#703 - Make experimental features public

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 2 comments

#702 - Remove unnecessary import

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 1 comment

#702 - Remove unnecessary import

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 1 comment

#701 - Unnecessary high-level import

Issue - State: closed - Opened by mattwthompson almost 2 years ago

#701 - Unnecessary high-level import

Issue - State: closed - Opened by mattwthompson almost 2 years ago

#700 - Add v0.3.1 release notes

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 1 comment

#700 - Add v0.3.1 release notes

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 1 comment

#699 - Document experimental features

Issue - State: closed - Opened by mattwthompson almost 2 years ago - 1 comment
Labels: documentation

#699 - Document experimental features

Issue - State: closed - Opened by mattwthompson almost 2 years ago - 1 comment
Labels: documentation

#698 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago - 1 comment

#697 - Store constraints in `from_openmm`

Pull Request - State: closed - Opened by mattwthompson almost 2 years ago - 2 comments