Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations

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 <i>k</i>_B<i>T</i>/6<i>ηV</i> with <i>k</i>_B Boltzmann’s constant, <i>T</i> the absolute temperature, η the solvent shear viscosity, and <i>V</i> 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