TCB Publications - Abstract

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.

NELS96 NAMD 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.

Download Full Text

The manuscripts available on our site are provided for your personal use only and may not be retransmitted or redistributed without written permissions from the paper's publisher and author. You may not upload any of this site's material to any public server, on-line service, network, or bulletin board without prior written permission from the publisher and author. You may not make copies for any commercial purpose. Reproduction or storage of materials retrieved from this web site is subject to the U.S. Copyright Act of 1976, Title 17 U.S.C.

Download full text: PDF (13.7MB), PS (115.0KB)