期刊
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
卷 9, 期 11, 页码 2874-2878出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jpclett.8b01090
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- Max Planck Society
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 k(B)T/6 eta V with k(B) Boltzmann's constant, T the absolute temperature, eta 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.
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