Comments (4)
I'm guessing this has to do with periodic boundary conditions; the ligand is being draw with the first atom at 0,0,0, but happens to be built with negative coordinates, whereas the water is filled in with positive coordinates. But if you consider periodic copies, it's fine. You would probably need to post the actually pdb to see.
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Thanks for your response!
I have uploaded the pdb file for reference at this repo link, where I only changed the step parameter in the ipynb file (from 5000 to 10000, hence there will be 20 MODELS in the pdb file).
From the pdb, it can be seen that the ligand is outside the edge of the water box in all 20 MODELS. However, as you mentioned, the simulation did not encounter any problems, so I wonder if I can disregard this odd visualization issue.
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Yes, I think you can
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Yes this looks like a quirk of visualization. Visualization/analysis tools usually have ways to move molecules between periodic images.
If the simulation runs, it's not likely an issue of the system being prepared wrong.
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Related Issues (20)
- 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 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
- PACKMOL wrapper with >100,000 atoms HOT 5
- Make `Interchange.topology` required? HOT 1
- LAMMPS atom writer makes assigning unique IDs to chemically-identical molecules impossible HOT 2
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