Harmonic analysis of large systems. I. Methodology

Authors

  • Bernard R. Brooks,

    Corresponding author
    1. Laboratory of Structural Biology / DCRT, National Institutes of Health, Bethesda, Maryland 20892
    • Laboratory of Structural Biology / DCRT, National Institutes of Health, Bethesda, Maryland 20892
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  • Dušanka Janežič,

    1. National Institute of Chemistry, Hajdrihova 19, 61115 Ljubljana, Slovenia
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    • Fulbright Scholar at the National Institutes of Health on leave from the National Institute of Chemistry, Ljubljana, Slovenia

  • Martin Karplus

    1. Chemistry Department, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 01238
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Abstract

Methods have been developed for the determination of vibrational frequencies and normal modes of large systems in the full conformational space (including all degrees of freedom) and in a reduced conformational space (reducing the number of degrees of freedom). The computational method, which includes Hessian generation and storage, full and iterative diagonalization techniques, and the refinement of the results, is presented. A method is given for the quasiharmonic analysis and the reduced basis quasiharmonic analysis. The underlying principle is that from the atomic fluctuations, an effective harmonic force field can be determined relative to the dynamic average structure. Normal mode analysis tools can be used to characterize quasiharmonic modes of vibration. These correspond to conventional normal modes except that anharmonic effects are included. Numerous techniques for the analyses of vibrational frequencies and normal modes are described. Criteria for the analysis of the similarity of low-frequency normal modes is presented. The approach to determining the natural frequencies and normal modes of vibration described here is general and applicable to any large system. © 1995 John Wiley & Sons, Inc.

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