ligand always out of box in ligand_in_water.ipynb about openff-interchange HOT 4 CLOSED

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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