A revised method, based on the hierarchical clustering data analysis technique, is proposed as an improved approach to estimate the mean residence time (MRT) related to the interaction between a molecule and its solvent as described via molecular dynamics simulations. Besides the description of the methodology, it is shown that our revised approach improves significantly the MRT evaluation of a representative model of a family of magnetic resonance imaging contrast agents when compared with the MRT value obtained for the same system by adopting a standard technique.