1999 | OriginalPaper | Buchkapitel
Conformational Dynamics Simulations of Proteins
verfasst von : Markus Eichinger, Berthold Heymann, Helmut Heller, Helmut Grubmüller, Paul Tavan
Erschienen in: Computational Molecular Dynamics: Challenges, Methods, Ideas
Verlag: Springer Berlin Heidelberg
Enthalten in: Professional Book Archive
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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.