Comments (4)
Will look at this and your changes more closely later but you're probably running into the long-standing problem of using SMIRNOFF in "conventional" atom-typed infrastructure, namely the atom type explosion problem. It's the sort of problem that seems like it should be easy to wrangle but doesn't always work out like that - with some differences in how engines handle each. I forget (but hope I can pull up!) some of the more antagonistic cases that prevented me from going all the way with atom type de-duplication in the past.
This is all to say your issue is surely valid, I'm not surprised you're running into some performance issues, and I've even tagged this as something to better document (#607).
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Following the discussion in #606 the behaviour suggested in #962 can be made optional, by adding a flag to Interchange.to_gromacs(combine_atomtypes: bool = False)
. This will keep the possibility to write all possible atomtypes if needed, but will also give the users the possibility to reduce the memory load. This solution also does not put any constraintes on the core Interchange code, only to one particular exporter. This flag will also provide a direct way to test the functionality.
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Related Issues (20)
- Wrong "scale_14" read from .json file HOT 5
- "dOH" written incorrectly in `[ settles ]` section HOT 2
- How to check missing parameters before create_interchange? HOT 2
- Pass cosmetic attrs through to `Potential` objects HOT 3
- Missing v-site exceptions with plugins HOT 5
- `Interchange.from_openmm` should raise an exception if the topology doesn't match the system HOT 3
- ligand always out of box in ligand_in_water.ipynb HOT 4
- 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
- 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
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