Embedding proteins into the membranes#
GROMACS is capable of inserting the protein into pre-equilibrated lipid bilayers with minimal perturbation of the lipids using the method, which was initially described as a ProtSqueeze technique, 157 and later implemented as g_membed tool 158. Currently the functionality of g_membed is available in mdrun as described in the user guide.
This method works by first artificially shrinking the protein in the