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Visualizing conformations in molecular dynamics

Please always quote using this URN: urn:nbn:de:0297-zib-3859
  • The Monte Carlo simulation of the dynamics of complex molecules produces trajectories with a large number of different configurations to sample configuration space. It is expected that these configurations can be classified into a small number of conformations representing essential changes in the shape of the molecule. We present a method to visualize these conformations by point sets in the plane based on a geometrical distance measure between individual configurations. It turns out that different conformations appear as well-separated point sets. The method is further improved by performing a cluster analysis of the data set. The point-cluster representation is used to control a three-dimensional molecule viewer application to show individual configurations and conformational changes. The extraction of essential coordinates and visualization of molecular shape is discussed.

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Author:Christoph Best, Hans-Christian HegeORCiDGND
Document Type:ZIB-Report
Tag:Cluster Analysis; Conformations; Molecular Dynamics; Visualization
MSC-Classification:62-XX STATISTICS / 62-07 Data analysis
92-XX BIOLOGY AND OTHER NATURAL SCIENCES / 92Cxx Physiological, cellular and medical topics / 92C40 Biochemistry, molecular biology
92-XX BIOLOGY AND OTHER NATURAL SCIENCES / 92Exx Chemistry (For biochemistry, see 92C40) / 92E10 Molecular structure (graph-theoretic methods, methods of differential topology, etc.)
PACS-Classification:00.00.00 GENERAL / 07.00.00 Instruments, apparatus, and components common to several branches of physics and astronomy (see also each subdiscipline for specialized instrumentation and techniques) / 07.05.-t Computers in experimental physics; Computers in education, see 01.50.H- and 01.50.Lc; Computational techniques, see 02.70.-c; Quantum computation architectures and implementations, see 03.67.Lx; Optical computers, see 42.79.Ta / 07.05.Rm Data presentation and visualization: algorithms and implementation
Date of first Publication:1998/12/30
Series (Serial Number):ZIB-Report (SC-98-42)
Published in:A rev. vers. appeared under the title "Visualizing and Identifying Conformational Ensembles in Molecular Dynamics Trajectories" in: Computing in Science and Engineering 4 (3) May/June (2002), pp. 68-75
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