Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations

J Phys Chem Lett. 2018 Jun 7;9(11):2874-2878. doi: 10.1021/acs.jpclett.8b01090. Epub 2018 May 17.

Abstract

We show that the rotational dynamics of proteins and nucleic acids determined from molecular dynamics simulations under periodic boundary conditions suffer from significant finite-size effects. We remove the box-size dependence of the rotational diffusion coefficients by adding a hydrodynamic correction kB T/6 ηV with kB Boltzmann's constant, T the absolute temperature, η the solvent shear viscosity, and V the box volume. We show that this correction accounts for the finite-size dependence of the rotational diffusion coefficients of horse-heart myoglobin and a B-DNA dodecamer in aqueous solution. The resulting hydrodynamic radii are in excellent agreement with experiment.