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Conformational Dynamics Simulations of Proteins

Conference paper
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Part of the Lecture Notes in Computational Science and Engineering book series (LNCSE, volume 4)

Abstract

Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FAMUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales.

Keywords

Hierarchy Level Force Profile Rupture Force Fast Multipole Method Water Bridge 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 1999

Authors and Affiliations

  1. 1.Institut für Medizinische Optik, Theoretische BiophysikLudwig-Maximilians-Universität MünchenMünchenGermany

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