Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé,
Robert D. Skeel, and Klaus Schulten.
NAMD - A parallel, object-oriented molecular dynamics program.
International Journal of Supercomputer Applications and High
Performance Computing, 10:251-268, 1996.
NELS96NAMD is a molecular dynamics program designed for high performance simulations of large biomolecular systems on parallel computers. An object-oriented design implemented using C++ facilitates the incorporation of new algorithms into the program. NAMD uses spatial decomposition coupled with a multithreaded, message-driven design which is shown to scale efficiently to multiple processors. Also, NAMD incorporates the Distributed Parallel Multipole Tree Algorithm for computation of 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-DNA -water complex of more 36,000 atoms illustrates the performance of NAMD.
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