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2. Calculating a molecular dynamics trajectory
For a system of N atoms, 6N values are needed to define the state of the system (three coordinate values and three velocity values per atom). Each combination of these values gives a point in 6N-dimensional space; this space is called phase space, and a trajectory configuration is therefore a collection of points in this space.
Molecular dynamics trajectory calculations are always performed under the ergodic assumption, i.e. that the average of a quantity over a set of equivalent particles is equal to the time average of a particle. This axiom of statistical mechanics makes it possible to calculate average system properties from a molecular dynamics simulation. If it were possible to visit all points in the phase space, the trajectory would be called ergodic and would not depend on the initial configuration. In practice, phase space is immense, and an ergodic trajectory...
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Calculating a molecular dynamics trajectory
Practical simulation methods
Bibliography
References
Main programs used and their force fields
Trajectory calculation programs are most often developed under the UNIX operating system. Biomolecule visualization and manipulation programs may be available under UNIX, Windows or Mac OS.
Three programs used in the molecular dynamics of biomacro-molecules are distributed to academic laboratories via a paying license:
GROMOS...
Computer configurations and computing times
To perform molecular dynamics calculations, the two most efficient configurations at present are: the use of a personal, single- or dual-processor workstation, or the use of a parallel machine or cluster.
The cheapest configurations are obtained by using a Linux PC or a cluster of Linux PCs. Parallel computers and clusters are offered by Silicon Graphics, Hewlett-Packard...
Organizations
The Groupe de Graphisme et Modélisation Moléculaire (GGMM) ( http://www.ibcp.fr/GGMM/ggmm.html ) aims to promote the development of computer-aided design applied to the study of biological macromolecules.
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