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NAMD - a Parallel, Object-Oriented Molecular Dynamics Program
| M. Nelson | William Humphrey | Attila Gursoy | A. Dalke | Laxmikant Kale | Robert Skeel | Klaus Schulten
International Journal Supercomputing Applications and High Performance Computing 1996
Publication Type: Paper
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Abstract
NAMD is a molecular dynamics program designed for high performance simulations of large biomolecular systems on parallel computers. An object-oriented design imple mented using C++ facilitates the incorporation of new algorithms into the program. NAMD uses spatial decom position coupled with a multithreaded, message-driven design, which is shown to scale efficiently to multiple processors. Also, NAMD incorporates the distributed par allel multipole tree algorithm for full electrostatic force evaluation in O(N) time. NAMD can be connected via a communication system to a molecular graphics program in order to provide an interactive modeling tool for viewing and modifying a running simulation. The application of NAMD to a protein-water system of 32,867 atoms illus trates the performance of NAMD.
TextRef
Mark Nelson and William Humphrey and Attila Gursoy and Andrew Dalke and Laxmikant Kale and Robert D. Skeel and Klaus Schulten, "NAMD-a Parallel, Object-Oriented Molecular Dynamics Program", Intl. J. Supercomput. Applics. High Performance Computing, Winter 1996, vol. 10, pp. 251-268.
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