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.
Author: | Konstantin Fackeldey, Susanna Röblitz, Olga Scharkoi, Marcus Weber |
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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 |