Genconf straightening out lipids?

[lipidsolidarity]

GROMACS version:
GROMACS modification: Yes/No
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Hi! I am trying to simulate a membrane with three types of molecules that I manually merged here:

The issue is when I run this command (hoping to create an 8 by 8 that is 6.4x6.4x9):

gmx genconf -f rowAB.gro -nbox 1 8 1 -o memAB.gro

It results in a rectangle that has straightened out the molecules and increased the distance between each row, making the membrane out of bounds for the box.

I’m not sure what is happening and what I can do to get a square slab that is 8 x 8 but also 6.4x6.4. Would genconf-ing the each molecule by 1 8 1 and then manually merging them be recommended? I understand that the molecules are extremely close to each other, but I thought these steric clashes would be resolved once I ran an energy minimization.

I’m not exactly sure what the best practice is here! Any advice or suggestions would be greatly appreciated.

[MagnusL]

Are you sure gmx genconf straightens out the molecules? It sounds strange. It should not modify the coordinates at all, just stack the box according to instructions. I’m not sure what you mean with that it has increased the distance between each row. The dimensions of each “copy” of the system should be exactly the dimensions of the input system. What is the box size of your input system? If you open the input system in VMD you should be able to verify this by visualizing the periodic images from the graphical representations. If you show 8 instances along in the y direction it should look like the output you get from gmx genconf.