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NAMD and molecular dynamics simulations

Molecular dynamics (MD) simulations compute atomic trajectories by solving equations of motion numerically using empirical force fields, such as the CHARMM force field, that approximate the actual atomic force in biopolymer systems. Detailed information about MD simulations can be found in several books such as [1,55]. In order to conduct MD simulations, various computer programs have been developed including X-PLOR [13] and CHARMM [12]. These programs were originally developed for serial machines. Simulation of large molecules, however, require enormous computing power. One way to achieve such simulations is to utilize parallel computers. In recent years, distributed memory parallel computers have been offering cost-effective computational power. NAMD was designed to run efficiently on such parallel machines for simulating large molecules. NAMD is particularly well suited to the increasingly popular Beowulf-class PC clusters, which are quite similar to the workstation clusters for which is was originally designed. Future versions of NAMD will also make efficient use of clusters of multi-processor workstations or PCs.

NAMD has several important features:


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