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Efficient Conformational Analysis by Partition-of-Unity Coupling
Please always quote using this URN: urn:nbn:de:0297-zib-42570
- Obtaining a sufficient sampling of conformational space is a common problem in molecular simulation. We present the implementation of an umbrella-like adaptive sampling approach based on function-based meshless discretization of conformational space that is compatible with state of the art molecular dynamics code and that integrates an eigenvector-based clustering approach for conformational analysis and the computation of inter-conformational transition rates. The approach is applied to three example systems, namely n-pentane, alanine dipeptide, and a small synthetic host-guest system, the latter two including explicitly modeled solvent.
Author: | Alexander Bujotzek, Ole Schütt, Adam Nielsen, Konstantin FackeldeyORCiD, Marcus Weber |
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Document Type: | ZIB-Report |
Parent Title (English): | Math Chem |
Tag: | Markov State Models; Meshfree; Molecular Simulation; Partition of Unity |
MSC-Classification: | 60-XX PROBABILITY THEORY AND STOCHASTIC PROCESSES (For additional applications, see 11Kxx, 62-XX, 90-XX, 91-XX, 92-XX, 93-XX, 94-XX) / 60Jxx Markov processes |
92-XX BIOLOGY AND OTHER NATURAL SCIENCES / 92-08 Computational methods | |
CCS-Classification: | G. Mathematics of Computing / G.4 MATHEMATICAL SOFTWARE |
G. Mathematics of Computing / G.3 PROBABILITY AND STATISTICS / Markov processes (NEW) | |
PACS-Classification: | 80.00.00 INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY / 87.00.00 Biological and medical physics / 87.10.-e General theory and mathematical aspects |
Date of first Publication: | 2013/09/27 |
Series (Serial Number): | ZIB-Report (13-58) |
ISSN: | 1438-0064 |
Licence (German): | Creative Commons - Namensnennung |