Generalized Langevin Methods
/Calculating position-dependent diffusion coefficients is a challenge for molecular simulation methods. We have implemented a simple method to compute this property by performing a simulation where the solute is restrained to a position. The diffusion coefficient can be estimated by analyzing the time series of that simulation based on the Generalized Langevin Equation. This is implemented in our code, ACFCalculator
Although this strategy is general, we present the theory and practical considerations in our paper where this method is used to calculation the rates of diffusion of solutes through membranes.
