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

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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.