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.