Flat bottomed position restraints as center of mass position restrains

GROMACS version: 2023.2
GROMACS modification: Yes/No
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I want to apply flat bottomed position restrains as center of mass position restraints for the protein-ligand complex embedded in its lipid bilayer. My requirement is to lower the movement of the protein within the bilayer in the xy plane.

Can someone tell me whether my method is suitable for my target and how do I apply flat bottomed posres using gm tools or other scripts?

Dear Dulaj,

Whether or not the procedure is suitable, that depends on your system and the question you want to answer. I can’t really help with such a general question, but you should take at least the time to explore a bit the scientific literature regarding your system of interest to check what they usually do, as this can save a lot of computational time.

How to technically achieve it, it again depends on what you are aiming for specifically. If you just want a flat bottomed potential along the direction/vector connecting the center of mass of protein/ligand and bilayer then you can implement it with GROMACS pull module. Take a look here. In you case, the relevant keyword would be pull-coord1-type=flat-bottom and then specify the two groups containing the pro/lig and bilayer.