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 FackeldeyORCiD, Susanna RöblitzORCiD, 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) |
| ZIB-Reportnumber: | 11-27 |
