GROMACS version: 2021.3
GROMACS modification: No
I have embedded in a protein in a membrane and started to equilibrate the system with the Martini 2.2 forcefield. I have noticed that there are significant bilayer undulations, but I would prefer the membrane to be planar.
Is there a way to add position restraints to only the lipids that are in the region near the edges of the box? I would like to try to pin the edges to a z location to flatten the membrane. My concern is that if I add headgroup restraints on all the lipids, the lipids will not fill in around the protein properly. Thank you for any suggestions.
You could add z restraints to a ~ 3 lipid deep perimeter to all the headgroup atoms in the lipid, but the undulations are so severe that I suspect the membrane would rupture . Without knowing how you got to this point or what the protein is - other than large and transmembrane… Abnormal strain on the membrane would likely also affect any alosteric effects of the lipids on the protein.
If the lipids in proximity to the protein are ’ where they want to be ’ and the membrane is not under any neg surface tension, I suggest building the model with about 1/4 of the lipids. bring that to equilibrium and rebuild with the next fraction of lipids, each new build should might maybe more planer. If the lipid type is not critical make the last layer different to make selection easier POPC vs POPE or DPPC.
hope this helps.
Thank you for your response. Here I have only energy minimized the structure, equilibrated under NVT conditions to 1 bar everywhere, and equilibrated under NPT conditions to 1 bar and ~310 K for ~100 ns. I haven’t added any surface tension to the membrane. Just to make sure I understand your second strategy, are you suggesting to build the protein in a lipid bilayer that is 1/4 the current size and then to embed that into a larger, fully equilibrated bilayer of single type lipids?