Uncertainty in MD-Derived Diffusion Coefficients Depends on Analysis Protocol, Not Just Simulation Data

Bonkowski and De Souza [Sol. Stat. Ionics 429, 116967 (2025)] provide a guide for performing molecular dynamics simulations of ion transport, including methods for estimating diffusion coefficients and their uncertainties from mean-squared displacement (MSD) data. However, they present the statistical properties of one specific analysis method---ordinary least squares (OLS) regression with particular data processing choices—without acknowledging this specificity, thereby implying these properties are universal characteristics of diffusion coefficient estimation. They also incorrectly characterise other literature methods as merely alternative ways to estimate the uncertainty in D*, when these methods actually estimate D* itself more precisely than simple OLS regression. Here, we clarify that for diffusion coefficients estimated by linear regression of MSD data, the uncertainty depends not only on the input simulation data, but also on the choice of statistical estimator and data processing decisions. We also comment on specific additional statements in Bonkowski and De Souza that may mislead readers.