Comments (3)
I think this is a holdover from the days when we thought that we could have a "pre-parameterization interchange" - Like, we could add two unparameterized molecules loaded from different places, and later apply a FF to them. We decided at some point that Interchanges would strictly be "post-parameterization", and in that context I think this ticket is totally closed. If there's a use case I'm not imagining here, folks can reopen this/open a new issue.
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Something to consider is that, when mixing two force fields from a line (i.e. Parsley), each SMIRKS in a potential handler is not guaranteed to be unique if not tracking the force field each is associated with. The SMIRKS patterns between versions of Parsley are mostly the same, and there is plenty of overlap between those and smirnoff99Frosst.
Maybe the best way to handle this is also track the source force field in the PotentialKey
objects.
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The __add__
functionality added in #148 may or may not do this clearly. I have not tested it yet. The Parsley + GAFF/ff19sb case should be mostly covered by testing if Parsley + Foyer-style force fields can co-exist.
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Related Issues (20)
- Loading topologies from OpenMM sometimes scrambles atom order HOT 2
- Electrostatics key mismatch after combination HOT 3
- Positions of `MonovalentLonePair` virtual sites is incorrect (does not affect simulations) HOT 1
- Virtual site parameters can clash if looked up using only SMIRKS HOT 4
- `experimental/openmmforcefields/gaff.ipynb` and `ligand_in_water.ipynb` notebooks broken on OpenFF Docs HOT 1
- units for `Interchange.collection['Bonds'].get_system_parameters()` HOT 2
- Support GROMACS's `3fad` virtual sites
- `get_positions_with_virtual_sites` does not collate virtual sites with molecules HOT 1
- Some combinations of Interchanges do not commute HOT 2
- Improved LAMMPS support. HOT 2
- LAMMPS versions prior to 2023.08.02 are incompatible with Interchange, but may be installed with it HOT 2
- Interchange.to_gromacs() creates a topology with far too many atomtypes, which influences GROMACS performance HOT 4
- Syncing topology and `Interchange` attributes
- Easier indexing into collections
- Look into ordering of charge dictionary
- Combining a Sage interchange with one loaded from OpenMM fails because the electrostatics cutoff is not set by the OpenMM importer, but is checked by the `combine` method HOT 1
- GROMACS writer chokes without unique molecule names HOT 5
- `experimental/openmmforcefields/gaff.ipynb` is failing on openff-docs HOT 3
- Dihedrals lost in `Interchange.from_gromacs` HOT 1
- PACKMOL wrapper with >100,000 atoms HOT 5
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