Part of the cation outside of the simulation box

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I have a system containing water and ionic liquid. After npt equilibration, I see that part of the molecule (for example tail of cation) located outside the simulation box.
Is this a problem in equilibration? If yes, how can solve this problem?
I tried equilibration by different simulation box or even change the cutoff value.
Please guide me if you have any experience


It’s unclear to me what you mean with “outside the box”. If you’re running with periodic boundary conditions any particle that is “outside” is, in fact, also inside the box at the other side. That’s not a problem, just the way the simulation works. Any Gromacs analysis tools should account for it.

If you have a molecule that is large enough that it’s comparable to the box size that might be a problem in itself. For such a case increasing the box size (and filling the new void with solvent) might be needed.


So thanks Petter for your reply. You’re right. I work with large molecule.
Your guidance was helpful.