dorsal/arxiv
View SchemaVisualizing Conformations in Molecular Dynamics
| Authors | Christoph Best, Hans-Christian Hege |
|---|---|
| Categories | |
| ArXiv ID | physics/9909049 |
| URL | https://arxiv.org/abs/physics/9909049 |
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.
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"abstract": "The Monte Carlo simulation of the dynamics of complex molecules produces\ntrajectories with a large number of different configurations to sample\nconfiguration space. It is expected that these configurations can be classified\ninto a small number of conformations representing essential changes in the\nshape of the molecule. We present a method to visualize these conformations by\npoint sets in the plane based on a geometrical distance measure between\nindividual configurations. It turns out that different conformations appear as\nwell-separated point sets. The method is further improved by performing a\ncluster analysis of the data set. The point-cluster representation is used to\ncontrol a three-dimensional molecule viewer application to show individual\nconfigurations and conformational changes. The extraction of essential\ncoordinates and visualization of molecular shape is discussed.",
"arxiv_id": "physics/9909049",
"authors": [
"Christoph Best",
"Hans-Christian Hege"
],
"categories": [
"physics.comp-ph",
"physics.bio-ph",
"physics.chem-ph",
"q-bio.BM"
],
"title": "Visualizing Conformations in Molecular Dynamics",
"url": "https://arxiv.org/abs/physics/9909049"
},
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