[gmx-users] Umbrella Sampling and PMF's

[Ilya Chorny]

Has anyone had experience with umbrella sampling using gromacs. I would
like to calculate the PMF between two amino acid side chains. I thought
of a way in which I could do it using free energy perturbation(dummy
atoms) but I would rather use umbrella sampling, but I'm not sure how to
constrain a the distance between two atoms in different molecules.

Ilya