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This paper introduces a residence-time approach (RTA) to compute position-dependent diffusivities from biased molecular dynamics simulations, specifically targeting trajectory segments with negligible effective drift. The RTA calculates local diffusivities directly from mean first-exit times out of finite spatial intervals, avoiding the need for harmonically restrained simulations or time-correlation function integration. Validated on oxygen diffusion across hexadecane, water permeation across lipid bilayers, and permeation of VOCs through skin membranes, the RTA demonstrates a practical alternative to fluctuation-based methods.
Ditch the noisy time-correlation functions: this new method extracts position-dependent diffusivities directly from biased molecular dynamics using residence times.
We introduce a residence-time approach (RTA) for determining position-dependent diffusivities from biased molecular dynamics simulations. The method is formulated for trajectory segments in which the effective drift along the transport coordinate is negligible, as realized here using adaptive biasing force simulations. In this regime, local diffusivities are obtained directly from mean first-exit times out of finite spatial intervals. Unlike conventional fluctuation-based approaches, the RTA does not require dedicated harmonically restrained simulations or numerical integration of noisy time-correlation functions. We assess the method for oxygen diffusion across a hexadecane slab, water permeation across a lipid bilayer, and permeation of water and selected volatile organic compounds through a model skin-barrier membrane. In the slab system, the RTA reproduces independently determined bulk diffusivities within statistical uncertainty. In the membrane systems, the inferred diffusivity profiles are supported by propagator-level validation. These results establish the RTA as a practical approach for extracting position-dependent diffusivities from biased molecular simulations.