Constructing a Memory Kernel of the Returning Probability to Efficiently Describe Molecular Binding Processes

Returning probability theory enables us to systematically analyze host-guest binding kinetics in terms of the thermodynamic and kinetic properties of the intermediate state existing in the binding processes with the molecular dynamics (MD) simulation. In order to employ this theory, we need to compute the returning probability, a time-correlation function for describing the kinetics of the intermediate state. Here, we present a methodology to realize the efficient calculation of the probability with the memory kernel construction.