Soft Versus Hard Metastable Conformations in Molecular Simulations

Please always quote using this URN: urn:nbn:de:0297-zib-13189
  • 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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Author:Konstantin Fackeldey, Susanna Röblitz, Olga Scharkoi, Marcus Weber
Document Type:ZIB-Report
Tag:Proteins, Conformation Space, Meshfree Methods
MSC-Classification:65-XX NUMERICAL ANALYSIS
92-XX BIOLOGY AND OTHER NATURAL SCIENCES
CCS-Classification:G. Mathematics of Computing
PACS-Classification:30.00.00 ATOMIC AND MOLECULAR PHYSICS
Date of first Publication:2011/06/22
Series (Serial Number):ZIB-Report (11-27)