GROMACS version: 2021.3
GROMACS modification: No
I want to prepare an asymmetric bilayer membrane using MARTINI FF. For this, I am preparing 2 symmetric bilayers - one representing the external leaflet of the asymmetric membrane (system A) and the second representing the cytoplasmic leaflet (system B). I equilibrate the 2 symmetric bilayer membranes and then want to combine one leaflet from system A and one from system B to get the final asymmetric membrane. However, when doing so, the two leaflets in the asymmetric membrane do not align. I tried aligning in VMD but that was of little help. Note that the two leaflets are of same dimensions in x and y directions. I am aware that insane and CHARMM-GUI can directly prepare the asymmetric bilayers but I would like to first equilibrate the symmetric bilayers to allow formation of lipid domains.
Can anyone please suggest me a way (Gromacs function, script, etc.) that can align the two leaflets to obtain the bilayer.