3. Practical simulation methods
The aim is to analyze a molecular dynamics trajectory and make the link with the experiment.
3.1 Choice of initial coordinates
The system's initial coordinates can have different origins:
(i) macromolecule structures determined by NMR or X-ray crystallography ;
(ii) construction of atomic coordinates using computer graphics software and values for bond lengths and angles (in silico construction);
(iii) structures predicted by bioinformatics.
Case (i) represents the situation of choice for starting a simulation, as it can be based on experimental structural information. System coordinates can often be downloaded...
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Practical simulation methods
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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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