Visualizing Conformations in Molecular Dynamics

Details Visualizing Conformations in Molecular Dynamics Visualizing Conformations in Molecular Dynamics

1999-09-23

arxiv.org/abs/physics/9909049v1

Physics

Computational Physics

13 pages, 8 figures, 1 color figure, LaTeX

Scientific paper

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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