Comments (2)
i hadn't read through this thoroughly: https://docs.openforcefield.org/projects/interchange/en/stable/using/collections.html. apologies, but thank you for the clarification!
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These are Pint-styled units from https://github.com/openforcefield/openff-units
I don't think I can make guarantees right now, but this is something to check. (This is the only part of the codebase that is sloppy with units, since I wasn't able to get JAX to understand them). Until then, the units are inspectable, albeit a little tucked away, in the API. In this case the units appear to match what's in the SMIRNOFF force field (AKMA-ish), if you're using a different source this might not be true:
In [22]: {
...: parameter.units
...: for potential in out["Bonds"].potentials.values()
...: for parameter in potential.parameters.values()
...: }
Out[22]: {<Unit('angstrom')>, <Unit('kilocalorie / angstrom ** 2 / mole')>}
In [23]: sage['Bonds'].parameters[-1]
Out[23]: <BondType with smirks: [#8:1]-[#1:2] id: b88 length: 0.9716763312559 angstrom k: 1087.053566377 kilocalorie / angstrom ** 2 / mole >
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Related Issues (20)
- Update GROMACS portion of ligand example
- 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
- 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 1
- 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
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