| If you are looking for a serious molecular dynamics code to run real simulations, there are several choices. Probably the most widely used and acclaimed molecular dynamics code is NAMD developed by the Theoretical and Computational Biophysics Group at the University of Illinois. NAMD is an open-source parallel molecular dynamics code primarily used to model large protein structures. It probably has the largest budget of all the MD codes available, for it has been run on the giant Tungsten Linux cluster at the NCSA. Another molecular dynamics code is AMBER, which is distributed by the University of California, San Francisco. AMBER is used to model large protein structures using force fields and methods not available in other codes. It is not open source, however, and can only be obtained in source code form on a CD. Finally, another popular MD code is GROMACS, an MD code distributed by the Department of Biophysical Chemistry at the Groningen University in the Netherlands. It is an open-source code that supports parallel processing and has been optimized to run on Linux machines using AMD or Intel processors. The makers of this code call GROMACS "The World's Fastest Molecular Dynamics" because it has beat other codes in performance tests.
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