Abstract
A revised method to compute mean residence time (MRT) from molecular dynamics (MD) simulations is reported. One of the most frequent scenarios in the modeling of biological related systems is to describe their interactions with the solvent that in most of the cases is water. This is important, for instance, in determining the three dimensional structure and function of proteins that will greatly depend on the affinity of certain sections of these biomolecules with water. The amount of interaction with water can be quantified by means of the so called MRT, which for this specific case is the average time that a water molecule stays within a certain distance (threshold) from a particular referential point of the model molecule.
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