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  Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations

Linke, M., Köfinger, J., & Hummer, G. (2018). Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations. The Journal of Physical Chemistry B, 122(21), 5630-5639. doi:10.1021/acs.jpcb.7b11988.

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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-Str. 1, 60438 Frankfurt am Main, Germany, ou_persistent22              

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 Abstract: We present a method to calculate the fully anisotropic rotational diffusion tensor from molecular dynamics simulations. Our approach is based on fitting the time-dependent covariance matrix of the quaternions that describe the rigid-body rotational dynamics. Explicit analytical expressions have been derived for the covariances by Favro, which are valid irrespective of the degree of anisotropy. We use these expressions to determine an optimal rotational diffusion tensor from trajectory data. The molecular structures are aligned against a reference by optimal rigid-body superposition. The quaternion covariances can then be obtained directly from the rotation matrices used in the alignment. The rotational diffusion tensor is determined by a fit to the time-dependent quaternion covariances, or directly by Laplace transformation and matrix diagonalization. To quantify uncertainties in the fit, we derive analytical expressions and compare them with the results of Brownian dynamics simulations of anisotropic rotational diffusion. We apply the method to microsecond long trajectories of the Dickerson–Drew B-DNA dodecamer and of horse heart myoglobin. The anisotropic rotational diffusion tensors calculated from simulations agree well with predictions from hydrodynamics.

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Language(s): eng - English
 Dates: 2018-01-242017-12-052018-01-302018-01-302018-05-31
 Publication Status: Published in print
 Pages: 10
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1021/acs.jpcb.7b11988
 Degree: -

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Title: The Journal of Physical Chemistry B
  Other : J. Phys. Chem. B
Source Genre: Journal
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Publ. Info: Washington, D.C. : American Chemical Society
Pages: - Volume / Issue: 122 (21) Sequence Number: - Start / End Page: 5630 - 5639 Identifier: ISSN: 1520-6106
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000293370_1