Overview
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Thérèse MALLIAVIN: CNRS research fellow - Theoretical Biochemistry Laboratory, Institut de Biologie Physico-Chimique (IBPC)
INTRODUCTION
Over the last twenty years or so, molecular dynamics simulations have taken off in biochemistry. This development is certainly linked to the development of computing and computer graphics resources, but has also benefited from the contribution of biophysical methods to the study of biomolecules at the atomic level. This article briefly outlines the principles of these molecular dynamics simulation methods and their application to biological macromolecules.
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Molecular dynamics simulations in biochemistry
Model frame
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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