Usefulness of Higher Order of System-Size Correction for Diffusion Coefficients of Macromolecules: A Molecular Dynamics Study

TL;DR

This study evaluates the accuracy of higher-order system-size correction methods for calculating diffusion coefficients of macromolecules in molecular dynamics simulations, highlighting limitations of simplified formulas in small simulation cells.

Contribution

It demonstrates the importance of higher-order corrections over simplified formulas for accurate diffusion coefficient estimation in small system simulations.

Findings

Simplified formulas can lead to inaccuracies in small systems.

Higher-order corrections improve the estimation of diffusion coefficients.

Discrepancies are explained through unsimplified correction formulas.

Abstract

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.