I am using GROMAC for MD, However I am not able to figure out how to select atoms or residues to apply a harmonic restraint.
At the active site there is a Cu ion and I want it remain there along with surrounding residues, water molecule and ligand so that it stays there in similar conformation during MD run. I don’t want it to fly away.
Is there any way to restrain the atoms and residues within a particular distance from specific atom e.g. copper?