Position Restraints on specific residues of a multimer

User discussions
1

GROMACS version: 2024
Hello everyone, I am struggling with implementing position constraints on specific residues of a multimer. The atom numbers in the topology and .gro file are different, when I use the .gro file indexes of the residues I get out of bound error. when I am using the atom numbers from to topol_chain.top file, it is not applying an restriction to the residues.
I checked by doing dump .tpr that it is showing position restraints on the whole protein chain instead. but still everything is moving and no restraints are implemented.

2

is it because of small force? did you added the restrain in topology and mdp file?

3

I tried the conventional fc of 1000. And I did add the restraints to the topology and mdp file. I want to have an idea that when we restraint some positions, does that mean it will not displace at all? Or more force less displacement? Also gromacs 2024 does not allow me to use a fc of more than 10000, and keeps on giving me errors of pressure coupling.