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Hello,
I generated a bacterial outer membrane using charmm gui. I simulated the membrane. Before i study the protein penetration into the membrane, I want to keep the edge of the membrane, that will not interact with the protein, fixed by limiting their movement and exert a force that keep the edge of the membrane stable and less influenced during the simulation. How could I do that, any suggestions? thanks
Why does your membrane have edges? If you use PBC (default), it will be an infinite 2D pseudo-crystal (repeating in space according to the box vectors).
Hello,
Thank you for your reply.
I would like to impose a stability and fixation on the membrane frame to be less influenced during the simulation of protein to membrane. How could I do that. thanks
Hi sabrine,
Certainly, you can modify the residue name of the atoms requiring position restraints in the coordinate file, for example, changing it to “PRS”. Afterward, you can use the make_ndx tool to construct an index file containing only the group with the “PRS” residue. Then, utilize genrestr to generate a topology file with position restraints.
I assume you’re inserting something like a single helix to figure out the affinity for the membrane? Inserting larger components might be tricky. Depending on the case, allowing your membrane to undulate/fluctuate might be crucial for describing the insertion though. But if that’s all you need, following the advice from @fizz should work, you can e.g. position-restrain only lipid heads, and/or only restrain them along the Z coordinate while allowing them to move in the XY plane.