How to control the thickness of lipid bilayer

I was trying to perform lipid bilayer MD for my protein based on GROMACS’s Membrane Protein Tutorial.

I can successfully orient the protein in the lipid (turquoise) as you can see in the image below:

But I would like to control the thickness A, B, C of the lipid, since I’d like to allow some area of the protein to be exposed outside the lipid (they’re extracellular region of the protein).

How can I achieve that with GROMACS?

This is not really a GROMACS question. The height of a bilayer is controlled by the type of lipid you use, the thermodynamic conditions and the quality of the force field. Any settings in a simulation code, apart from thermodynamic state parameters, have no effect on this height.

I don’t know how you generated the structure in the picture, but the height of the membrane might change a bit when you equilibrate the system.