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Comparative study of various normal mode analysis techniques based on partial Hessians
Authors:An Ghysels  Veronique Van Speybroeck  Ewald Pauwels  Saron Catak  Bernard R Brooks  Dimitri Van Neck  Michel Waroquier
Institution:1. Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, 9000 Gent, Belgium;2. Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
Abstract:Standard normal mode analysis becomes problematic for complex molecular systems, as a result of both the high computational cost and the excessive amount of information when the full Hessian matrix is used. Several partial Hessian methods have been proposed in the literature, yielding approximate normal modes. These methods aim at reducing the computational load and/or calculating only the relevant normal modes of interest in a specific application. Each method has its own (dis)advantages and application field but guidelines for the most suitable choice are lacking. We have investigated several partial Hessian methods, including the Partial Hessian Vibrational Analysis (PHVA), the Mobile Block Hessian (MBH), and the Vibrational Subsystem Analysis (VSA). In this article, we focus on the benefits and drawbacks of these methods, in terms of the reproduction of localized modes, collective modes, and the performance in partially optimized structures. We find that the PHVA is suitable for describing localized modes, that the MBH not only reproduces localized and global modes but also serves as an analysis tool of the spectrum, and that the VSA is mostly useful for the reproduction of the low frequency spectrum. These guidelines are illustrated with the reproduction of the localized amine‐stretch, the spectrum of quinine and a bis‐cinchona derivative, and the low frequency modes of the LAO binding protein. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
Keywords:Hessian  partial Hessian  NMA  normal modes  vibrational modes  mobile block Hessian  MBH  vibrational subsystem analysis  VSA  PHVA  RTB  partial optimization  LAO binding protein  cinchona
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