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An efficient analysis of rare events in canonical ensemble dynamics

Please always quote using this URN: urn:nbn:de:0297-zib-10871
  • For an analysis of a molecular system from a computational statistical thermodynamics point of view, extensive molecular dynamics simulations are very inefficient. During this procedure, at lot of redundant data is generated. Whereas the algorithms spend most of the computing time for a sampling of configurations within the basins of the potential energy landscape of the molecular system, the important information about the long-time behaviour of the molecules is given by transition regions and barriers between the basins, which are sampled rarely only. Thinking of molecular dynamics trajectories, researchers try to figure out which kind of dynamical model is suitable for an efficient simulation. This article suggests to change the point of view from extensive simulation of molecular dynamics trajectories to more efficient sampling strategies of the conformation dynamics approach.

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Author:Marcus Weber
Document Type:ZIB-Report
Tag:Kanonische Gesamtheit; Metastabilität; Moleküldynamik
canonical ensemble; metastability; molecular dynamics
PACS-Classification:00.00.00 GENERAL / 02.00.00 Mathematical methods in physics / 02.70.-c Computational techniques; simulations (for quantum computation, see 03.67.Lx; for computational techniques extensively used in subdivisions of physics, see the appropriate section; for example, see 47.11.-j Computational methods in fluid dynamics) / 02.70.Hm Spectral methods
Date of first Publication:2008/08/25
Series (Serial Number):ZIB-Report (08-36)
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