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.

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Author:Alexander Bujotzek, Ole Schütt, Adam Nielsen, Konstantin Fackeldey, Marcus Weber
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):License LogoCreative Commons - Namensnennung