GROMACS version: 2020.4
GROMACS modification: No
I’m trying to set up my simulations so that all water molecules are not allowed to get close to a defined water molecule in the binding site (with a distance cutoff). I think an inverted flat bottomed position restrict is a good choice. But as far as I understand, the flat-bottomed position restraints implemented in GROMACS only work on defined atoms themselves. So in this case I can only apply restraints to those bulk waters to their own positions but not to another water oxygen (named as a different molecule type) through defining Ri in the position_restraint section in my topology file. Is that correct? If so, is there another way in GROMACS can achieve what I’m trying to do here?