GROMACS version: 2026.1
GROMACS modification: No
Hello!
I am running an SMD on a multidomain and quite large protein. I have restrained one residue on one side, and I want to pull form teh other side on two C termini, to make it a physiological as possible. I am afraid that due to the protein size, just pulling on the end residues may destabilise it, so I want to lock in the two domains together with a distance restraint. However, I am struggling to do this. Should I add it as a new pull coordinate, or is there a way I can add it to the topology files in initialization. fyi: this two domains are on seperate chains, so it’s two separate topology files.
I am thinking about flat bottom potential here