I was trying to perform an MD of a protein (Mrgprx2) in a lipid bilayer.
The domain of the protein looks like this:
Thus I'd like to have the transmembrane part of the protein to be buried in lipid membrane, and the extracellular part of it to be placed outside membrane.
I was following the Gromacs Membrane Protein Tutorial.
However the protein orientation I get is not as I expected:
Notice that the whole protein is buried in the lipid and in tilted position instead of perpendicular with respect to the lipid bilayer. How can I properly orient the protein in the membrane?