385 eng reportzib 0 1998-12-30 1998-12-30 -- 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. SC-98-42 386 urn:nbn:de:0297-zib-3859 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 Christoph Best Hans-Christian Hege SC-98-42 eng uncontrolled Molecular Dynamics eng uncontrolled Conformations eng uncontrolled Visualization eng uncontrolled Cluster Analysis Informatik, Informationswissenschaft, allgemeine Werke Data presentation and visualization: algorithms and implementation Data analysis Biochemistry, molecular biology Molecular structure (graph-theoretic methods, methods of differential topology, etc.) ZIB Allgemein Hege, Hans-Christian https://opus4.kobv.de/opus4-zib/files/385/SC-98-42.ps https://opus4.kobv.de/opus4-zib/files/385/SC-98-42.pdf