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Soft Versus Hard Metastable Conformations in Molecular Simulations

Please always quote using this URN:urn:nbn:de:0296-matheon-10307
  • Particle methods have become indispensible in conformation dynamics to compute transition rates in protein folding, binding processes and molecular design, to mention a few. Conformation dynamics requires at a decomposition of a molecule's position space into metastable conformations. In this paper, we show how this decomposition can be obtained via the design of either ``soft'' or ``hard'' molecular conformations. We show, that the soft approach results in a larger metastabilitiy of the decomposition and is thus more advantegous. This is illustrated by a simulation of Alanine Dipeptide.

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Metadaten
Author:Konstantin Fackeldey, Susanna Röblitz, Olga Scharkoi, Marcus Weber
URN:urn:nbn:de:0296-matheon-10307
Referee:Peter Deuflhard
Document Type:Preprint, Research Center Matheon
Language:English
Date of first Publication:2012/01/27
Release Date:2012/01/27
Institute:Zuse Institute Berlin (ZIB)
MSC-Classification:65-XX NUMERICAL ANALYSIS / 65Lxx Ordinary differential equations / 65L15 Eigenvalue problems
Preprint Number:882
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