SC 98-42 Christoph Best, Hans-Christian Hege: Visualizing conformations in molecular dynamics
Abstract: 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.
Keywords: Molecular Dynamics,
Conformations,
Visualization,
Cluster Analysis
MSC: 62-07, 92E10, 92C40
PACS: 07.05.Rm, 87.15.He