Dear @obZehn ,
Thank you very much for the valuable information you provided!
Could you please tell me how I set the flat-bottomed position restrains using one of the gromacs commands such as gmx genrestr ? Or should I use a script (eg; Python script) ?
Also, as you have mentioned in this part, my justification is that I’m applying flat-bottomed position restraints as a centre of mass position restraints (I mean that I want to keep the protein channel without moving everywhere in the lipid membrane by applying a force to the centre of mass.). Even for a part of the equilibration to avoid moving the protein due to unequilibrated lipids.
I did some MD simulations with the protein embedded in a POPE bilayer. I observed sometimes protein had moved through the bilayer. Since I’m going to use smaller X and Y lengths of the lipid bilayer to decrease the computational cost, I’m afraid that the protein would be moved through the bilayer to reach the box boundaries. Even with PBC, it was harder for me to centre the protein in that bilayer system than in the process of centring the protein when it is simulated in a water box (for example when calculating RMSD.