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 \(xy\)-plane, then it removes lipids that overlap with that much smaller core. Then the protein atoms are gradually resized back to their initial configuration, using normal dynamics for the rest of the system, so the lipids adapt to the protein. Further lipids are removed as required.