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  Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations

Linke, M., Köfinger, J., & Hummer, G. (2018). Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations. The Journal of Physical Chemistry Letters, 9(11), 2874-2878. doi:10.1021/acs.jpclett.8b01090.

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Genre: Journal Article

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 Creators:
Linke, Max1, Author              
Köfinger, Jürgen1, Author              
Hummer, Gerhard1, 2, Author              
Affiliations:
1Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society, ou_2068292              
2Department of Physics, Goethe University Frankfurt, Max-von-Laue-Straße 1, 60438 Frankfurt am Main, Germany, ou_persistent22              

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 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 kBT/6ηV 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.

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Language(s): eng - English
 Dates: 2018-04-092018-05-112018-05-112018-06-07
 Publication Status: Published in print
 Pages: 5
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1021/acs.jpclett.8b01090
 Degree: -

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Title: The Journal of Physical Chemistry Letters
  Abbreviation : J. Phys. Chem. Lett.
Source Genre: Journal
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Publ. Info: Washington, DC : American Chemical Society
Pages: - Volume / Issue: 9 (11) Sequence Number: - Start / End Page: 2874 - 2878 Identifier: CoNE: https://pure.mpg.de/cone/journals/resource/1948-7185