defines the probability of finding a particle at a distance 'r' from a reference center. We use this formalism to compute the probability distribution of cations within 10 Å of carboxyl, acetyl and hydroxyl functional groups. The built-in radial pair distribution function (RDF) within VMD 1.9.4a58 45 is used to quantify the distance based probability, from the nearest neighbor list interactions computed for each frame of the equilibrium trajectory.