openforcefield openff-interchange issues

openforcefield / openff-interchange

A project (and object) for storing, manipulating, and converting molecular mechanics data.

https://docs.openforcefield.org/projects/interchange

MIT License

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issues

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Fix default `.charges`

#1066 mattwthompson opened 1 day ago
2
Error if HMR results in negative particle mass

#1065 mattwthompson opened 1 day ago
1
Document that topology charges are ignored

#1064 mattwthompson opened 4 days ago
1
Support of virtual sites for creating an Interchange `from_openmm`

#1063 hannahbaumann opened 5 days ago
2
Packmol interface: can't pack mnsol benchmark inputs with assumed evaluator defaults

#1062 IAlibay opened 6 days ago
7
`_apply_hmr` can silently lead to negative values

#1061 IAlibay opened 1 week ago
3
[ENH] add hydrogen_mass and ewald_tolerance to `to_openmm_simulation`

#1060 IAlibay opened 1 week ago
1
`from_smirnoff` _without_ `charge_from_molecules` silently assigns all isormophic molecules the same partial charges

#1059 IAlibay opened 1 week ago
5
`charge_from_molecules` silently ignores isomorphic molecules in list, only using the first entry

#1058 IAlibay opened 1 week ago
2
Passing a Molecule without charges to `from_smirnoff`'s `charge_from_molecules` fails ungracefully

#1057 IAlibay opened 1 week ago
1
[ENH] Add support for HMR with virtual sites

#1056 IAlibay opened 1 week ago
1
[DOCS] Document HMR virtual site limitation

#1055 IAlibay opened 1 week ago
0
`to_openmm_positions` includes virutal sites but `Interchange.positions.to_openmm()` does not

#1054 IAlibay opened 1 week ago
2
Log charge assignment

#1053 mattwthompson opened 1 week ago
3
`SMIRNOFFElectrostaticsCollection.charges` does not report cached charges

#1052 mattwthompson opened 1 week ago
0
Update topology/system particle bookkeeping in OpenMM

#1051 mattwthompson opened 2 weeks ago
2
Partial charge assignment using `charge_from_molecules` on virtual sites / charge increments can be unexpected.

#1050 IAlibay opened 2 weeks ago
8
Created OpenMM Topology and System virtual site atom indices don't match

#1049 IAlibay opened 2 weeks ago
6
[ENH] Improve logging / user experience for charge assignment

#1048 IAlibay opened 2 weeks ago
4
[pre-commit.ci] pre-commit autoupdate

#1047 pre-commit-ci[bot] opened 4 weeks ago
1
Add amber example

#1046 mattwthompson closed 1 month ago
2
Fix charge ordering in `.prmtop` files

#1045 mattwthompson closed 1 month ago
1
[pre-commit.ci] pre-commit autoupdate

#1044 pre-commit-ci[bot] closed 1 month ago
1
API cleanup

#1043 mattwthompson closed 1 month ago
2
Clarify `to_openmm_simulation` docstring and rename `to_lammps(file_path)` arg to `prefix`

#1042 Yoshanuikabundi opened 1 month ago
0
Add `to_amber` convenience method

#1041 mattwthompson closed 1 month ago
1
[pre-commit.ci] pre-commit autoupdate

#1040 pre-commit-ci[bot] closed 1 month ago
1
Support reaction field electrostatics in OpenMM

#1039 mattwthompson closed 1 month ago
1
Add `Interchange.to_amber`

#1038 mattwthompson closed 1 month ago
0
Test that atom names are processed in `Interchange.from_openmm`

#1037 mattwthompson closed 1 month ago
3
Protein water systems

#1036 lwhitm1 closed 1 month ago
1
Fix access to `_NonbondedData` NamedTuple

#1035 JMorado closed 1 month ago
9
Do not write vacuum simulations to GROMACS files

#1034 mattwthompson closed 1 month ago
2
Fix ordering of charges in CHARGE section when using to_prmtop

#1033 lukasbaldauf closed 1 month ago
10
Migrate formatting to `ruff`

#1032 mattwthompson closed 1 month ago
2
Loosing Gromacs atom name details when using an OpenMM topology

#1031 hannahbaumann closed 1 month ago
5
[pre-commit.ci] pre-commit autoupdate

#1030 pre-commit-ci[bot] closed 1 month ago
1
Status of vacuum simulations in GROMACS

#1029 mattwthompson closed 1 month ago
5
GROMACS Residue IDs not incremented when writing multiple copies of a unique molecule

#1028 mattwthompson closed 1 month ago
0
Convenience methods for producing run input files

#1027 Yoshanuikabundi closed 1 month ago
10
Simplify access to Pydantic v1 API

#1026 mattwthompson closed 1 month ago
1
[pre-commit.ci] pre-commit autoupdate

#1025 pre-commit-ci[bot] closed 1 month ago
1
Test more cases of handling GROMACS residue IDs

#1024 mattwthompson closed 1 month ago
3
Fix indexing in vdW lookup of atoms in GROMACS export

#1023 mattwthompson closed 2 months ago
2
GROMACS export crashes due to non-bonded lookup failures when virtual sites are present in some topologies

#1022 megosato closed 2 months ago
2
[pre-commit.ci] pre-commit autoupdate

#1021 pre-commit-ci[bot] closed 2 months ago
1
Add basic performance tests

#1020 mattwthompson opened 2 months ago
0
Improve GROMACS export performance in special case

#1019 mattwthompson closed 2 months ago
2
Improve speed of writing large molecules to GROMACS

#1018 mattwthompson closed 2 months ago
4
[pre-commit.ci] pre-commit autoupdate

#1017 pre-commit-ci[bot] closed 2 months ago
1