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Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach

J. Chem. Phys. 130, 084107 (2009); doi:10.1063/1.3071261

Published 25 February 2009

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A. Ghysels,1 D. Van Neck,1 B. R. Brooks,2 V. Van Speybroeck,1 and M. Waroquier1
1Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, B-9000 Gent, Belgium
2Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
In a previous paper [Ghysels et al., J. Chem. Phys. 126, 224102 (2007)] the mobile block Hessian (MBH) approach was presented. The method was designed to accurately compute vibrational modes of partially optimized molecular structures. The key concept was the introduction of several blocks of atoms, which can move as rigid bodies with respect to a local, fully optimized subsystem. The choice of the blocks was restricted in the sense that none of them could be connected, and also linear blocks were not taken into consideration. In this paper an extended version of the MBH method is presented that is generally applicable and allows blocks to be adjoined by one or two common atoms. This extension to all possible block partitions of the molecule provides a structural flexibility varying from very rigid to extremely relaxed. The general MBH method is very well suited to study selected normal modes of large macromolecules (such as proteins and polymers) because the number of degrees of freedom can be greatly reduced while still keeping the essential motions of the molecular system. The reduction in the number of degrees of freedom due to the block linkages is imposed here directly using a constraint method, in contrast to restraint methods where stiff harmonic couplings are introduced to restrain the relative motion of the blocks. The computational cost of this constraint method is less than that of an implementation using a restraint method. This is illustrated for the alpha-helix conformation of an alanine-20-polypeptide. ©2009 American Institute of Physics
History: Received 11 November 2008; accepted 22 December 2008; published 25 February 2009
Permalink: http://link.aip.org/link/?JCPSA6/130/084107/1
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KEYWORDS and PACS

Keywords
PACS
  • 36.20.Ng
    Vibrational and rotational structure, infrared and Raman spectra of macromolecules
  • 33.15.Mt
    Molecular rotation, vibration, and vibration-rotation constants
  • 33.20.Tp
    Vibrational analysis (molecular spectra)
  • 33.15.Bh
    General molecular conformation and symmetry; stereochemistry
  • 36.20.Hb
    Macromolecular configuration (bonds, dimensions)
  • YEAR: 2009

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PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
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