1. Model frame
Molecular dynamics simulations are carried out on an isolated macromolecule or macromolecular complex. On a scale of a few nanometers, a solution or solid is represented by the set of coordinates of its component atoms, so that the trajectories of these coordinates over time can be simulated using a computer. Molecular dynamics simulation methods were developed in theoretical liquid physics in the 1980s
One of the aims of molecular modeling is to compare the energies of the conformers of a molecule. The most rigorous...
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Model frame
Calculating a molecular dynamics trajectory
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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