Ecosyste.ms: Issues

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GitHub / openforcefield/openff-interchange issues and pull requests

#696 - `from_openmm` does not process constraints

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

#695 - Support plugin vdW interactions without electrostatics

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

#694 - Support custom non-bonded functional forms without electrostatics handlers

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

#693 - Incorrect 1-4 vdW energies differences with OpenMM

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

#692 - Tag some features as opt-in experimental

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

#691 - Wire `combine_nonboned_forces` through to `get_summary_data`

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

#690 - `get_openmm_energies` does not respect `combine_nonbonded_forces=False`

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

#689 - Make PACKMOL wrapper pseudo-private

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

#688 - Unclear relationships between intermolecular exclusions, 1-4 pairs, proper torsions, and improper torsions in Amber files

Issue - State: open - Opened by mattwthompson almost 2 years ago - 4 comments
Labels: help wanted, feedback needed

#687 - Document usage of `openff.interchange.drivers` module

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

#686 - Incorrect nonbonded energies from Amber if improper torsions are present

Issue - State: open - Opened by mattwthompson almost 2 years ago - 4 comments
Labels: bug, help wanted

#685 - Fix non-bonded interactions in Amber export

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

#684 - Fix docs environment and tidy up pack_box docstring

Pull Request - State: closed - Opened by Yoshanuikabundi almost 2 years ago - 7 comments

#683 - Test topology isomorphism with simple molecules

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

#682 - Saved Amber files when loaded report different non bonded energies

Issue - State: closed - Opened by bieniekmateusz almost 2 years ago - 11 comments

#681 - Copy PACKMOL wrapper from OpenFF Evaluator

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

#680 - Fix text wrapping and exclusions in Amber export

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

#679 - Duplicate excluded atom pairs in Amber export

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

#678 - Atom names can be mangled in Amber export

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

#677 - Add conversion `GROMACSSystem` -> `Interchange`

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

#675 - Update `mypy` pin

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

#674 - Update betas workflow

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

#673 - Add vectorized representation example

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

#673 - Add vectorized representation example

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

#672 - Port PACKMOL wrapper from OpenFF Evaluator

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

#672 - Port PACKMOL wrapper from OpenFF Evaluator

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

#671 - Simplify wrapping GROMACS exporters

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

#670 - Add methods for adding and removing GROMACS molecules

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

#668 - Support re-assignment in `GROMACSSystem.molecule_types`

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

#667 - Support cut-off electrostatics

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

#665 - Write `[ settles ]`

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

#664 - Implement `[ settles ]` for water molecules from SMIRNOFF

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

#663 - Improve speed of Amber export

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

#662 - Privatize tests and un-tested modules

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

#661 - Speed up Amber export

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

#660 - Shuffle Foyer module, update type annotations for Python 3.9+

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

#660 - Shuffle Foyer module, update type annotations for Python 3.9+

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

#659 - Test `from_openmm`

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

#658 - Make GROMACS export compatible with `_SimpleMolecule`

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

#657 - Remove tests from public API

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

#656 - Use constrained force field when testing energy reporters

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

#655 - Attempt to always write RESIDUE_LABEL

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

#654 - Create module for base `Collection` classes

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

#653 - Fix/clean up some annotations

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

#652 - Missing RESIDUE_LABEL flag in AMBER topology

Issue - State: closed - Opened by lohedges almost 2 years ago - 9 comments
Labels: bug

#652 - Missing RESIDUE_LABEL flag in AMBER topology

Issue - State: closed - Opened by lohedges almost 2 years ago - 9 comments
Labels: bug

#651 - Support multiple `ParameterHandler`s in one `SMIRNOFFCollection` plugin

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

#650 - Fix docs builds

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

#650 - Fix docs builds

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

#649 - Remove use of `pkg_resources`

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

#648 - Support multiple `ParameterHandlers` in one `SMIRNOFFCollection`

Pull Request - State: closed - Opened by wwilla7 almost 2 years ago - 4 comments

#647 - Support multiple `ParameterHandler`s in one `SMIRNOFFCollection`

Issue - State: closed - Opened by wwilla7 almost 2 years ago - 3 comments
Labels: enhancement, plugins

#646 - Ensure residue names are set from SMIRNOFF to GRO files

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

#645 - Support Python 3.11

Issue - State: open - Opened by mattwthompson almost 2 years ago - 1 comment
Labels: enhancement, dependencies

#644 - Bring installation guide in line with ecosystem docs

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

#643 - Automatically detect API changes

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

#639 - Update supported Python versions to 3.9-3.10

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

#638 - Investigate energy differences

Issue - State: closed - Opened by mattwthompson almost 2 years ago - 1 comment
Labels: good first issue

#633 - Begin supporting InterMol-styled `MDConfig`

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

#632 - Improve evaluation of bond constraints in LAMMPS exports

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

#631 - Assorted fixes

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

#626 - Add high-level method for transforming into "InterMol settings"

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

#623 - Unclear how to split OpenMM torsion energies between propers and impropers

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

#623 - Unclear how to split OpenMM torsion energies between propers and impropers

Issue - State: open - Opened by mattwthompson almost 2 years ago - 1 comment
Labels: help wanted, question, feedback needed

#620 - `openmm.NonbondedForce` does not respect `vdWHandler.cutoff` in the gas phase

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

#612 - Lint Markdown files

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

#600 - Torsion energy mismatch with GROMACS

Issue - State: closed - Opened by mattwthompson almost 2 years ago - 5 comments
Labels: bug

#595 - Handle Buckingham potentials with a plugin, not as a special case

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

#579 - Support geometric mixing rule in OpenMM export

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

#567 - Add examples visualizing molecules with virtual sites

Pull Request - State: open - Opened by mattwthompson about 2 years ago - 2 comments

#552 - Comparing the openMM and Gromacs energy

Issue - State: closed - Opened by xiki-tempula over 2 years ago - 5 comments

#552 - Comparing the openMM and Gromacs energy

Issue - State: open - Opened by xiki-tempula over 2 years ago - 4 comments

#516 - Speed up `Interchange` creation

Issue - State: closed - Opened by mattwthompson over 2 years ago - 10 comments

#515 - Defer pandas imports

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

#478 - Add convenience method for exporting positions with virtual sites

Issue - State: closed - Opened by mattwthompson over 2 years ago - 3 comments

#369 - Make `openff.interchange.interop.internal` private

Issue - State: closed - Opened by SimonBoothroyd about 3 years ago - 3 comments

#366 - SMIRNOFF handlers don't inherit `BaseXXXHandler` classes

Issue - State: closed - Opened by SimonBoothroyd about 3 years ago - 3 comments

#356 - Another thing people use ParmEd for - translate data into a richer format for use in VMD.

Issue - State: open - Opened by mrshirts about 3 years ago - 1 comment
Labels: enhancement

#307 - Units: Some duck-typed quantities are not processed as expected

Issue - State: closed - Opened by mattwthompson over 3 years ago - 1 comment

#264 - Design: Term-specific TopologyKey subclasses?

Issue - State: closed - Opened by mattwthompson over 3 years ago - 3 comments

#264 - Design: Term-specific TopologyKey subclasses?

Issue - State: closed - Opened by mattwthompson over 3 years ago - 3 comments

#249 - Angle energy mismatch between GROMACS and Amber

Issue - State: open - Opened by mattwthompson over 3 years ago - 6 comments
Labels: help wanted

#239 - Cleanup: Slow import times

Issue - State: open - Opened by mattwthompson over 3 years ago - 3 comments

#239 - Cleanup: Slow import times

Issue - State: open - Opened by mattwthompson over 3 years ago - 3 comments

#133 - Tests: Port some existing tests from OpenFF Toolkit

Issue - State: closed - Opened by mattwthompson almost 4 years ago - 1 comment

#133 - Tests: Port some existing tests from OpenFF Toolkit

Issue - State: closed - Opened by mattwthompson almost 4 years ago - 1 comment

#103 - SMIRNOFF: Resolving nonbonded methods

Issue - State: closed - Opened by mattwthompson about 4 years ago - 3 comments

#68 - Serialization: JSON

Issue - State: closed - Opened by mattwthompson about 4 years ago - 1 comment
Labels: blocked by topology refactor

#58 - Design: Structure of interoperability layer

Issue - State: closed - Opened by mattwthompson about 4 years ago - 3 comments

#35 - Enforcing order of potential handlers

Issue - State: closed - Opened by mattwthompson over 4 years ago - 4 comments

#34 - "meta" handlers

Issue - State: closed - Opened by mattwthompson over 4 years ago - 4 comments

#32 - More complex slot-parameter mapping

Issue - State: closed - Opened by mattwthompson over 4 years ago - 3 comments