Solvating protein and molecule in box creating overlap

GROMACS version: 2020.1
GROMACS modification: No

I am a bit new to GROMACS and I am trying to run a simulation of molecules diffusing through a protein pore. Currently, I have two rectangular boxes of same dimension (6.41840 6.44350 13.19300) with my protein and molecules centered at different ends (z = 1.649125 and 9.89475). When I try to use gmx solvate with the two boxes, an overlap occurs.

I’ve tried solvating with a greater z distance between the two (box z = 20, with centers z = 1 and 18) , but an overlap occurs. Interestingly, when I solvated the two boxes with the protein centered at a corner of its box, an overlap did not occur.

Not sure what is going on here, but any help would be appreciated.
Thank you,

Did you try to check how it looks in programs for visualization like Pymol or VMD? PyMOL |