Usefulness of higher-order system-size correction for macromolecule diffusion coefficients: A molecular dynamics study

Yeh and Hummer’s simplified estimation method has often been adopted to obtain diffusion coefficients for solute molecules using molecular dynamic simulation. However, the simplified formula is not necessarily valid when a small basic cell is used. Therefore, we conducted molecular dynamics simulations of aqueous protein solution to estimate the diffusion coefficient for the infinite dilution limit. We confirmed a deviation from the simplified formula in the simulation data and rationalized the discrepancy based on the unsimplified formula. [Display omitted] •Macromolecular diffusion coefficients depend on the system volume.•Deviation from conventional Yeh–Hummer method and the rationalization.•An approach to estimate the diffusion coefficient for the infinite dilution limit.