Accurate Estimation of Diffusion Coefficients and their Uncertainties from Computer Simulation.

ABSTRACT: Self-diffusion coefficients, D*, are routinely estimated from molecular dynamics simulations by fitting a linear model to the observed mean squared displacements (MSDs) of mobile species. MSDs derived from simulations exhibit statistical noise that causes uncertainty in the resulting estimate of D*. An optimal scheme for estimating D* minimizes this uncertainty, i.e., it will have high statistical efficiency, and also gives an accurate estimate of the uncertainty itself. We present a scheme for estimating D* from a single simulation trajectory with a high statistical efficiency and accurately estimating the uncertainty in the predicted value. The statistical distribution of MSDs observable from a given simulation is modeled as a multivariate normal distribution

SUBMITTER: McCluskey AR 

PROVIDER: S-EPMC11736684 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature