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Proceedings of the 1999 ACM/IEEE conference on Supercomputing
Large Scale Molecular Dynamics Simulations with Fast Multipole Implementations
Portland, Oregon, USA
November 13-November 18
ISBN: 1-58113-091-0
Zhiqiang Wang, AFRL/MLPJ
James Lupo, AFRL/MLPJ
Alan McKenney, AFRL/MLPJ
Ruth Pachter, AFRL/MLPJ
We present the performance of the fast molecular dynamics (FMD) code designed for efficient, object-oriented, and scalable large scale molecular simulations. FMD uses an implementation of the three-dimensional fast multipole method, FMM3D, developed in our group. The Fast Multipole Method offers an efficient way (order O(N)) to handle long range electrostatic interactions, thus enabling a more realistic molecular dynamics simulation of large molecular systems. The performance testing was carried out on IBM SP2, SGI Origin 2000, and CRAY T3E systems with the MPI message passing system. Two models, a random charged particle model of up to 100,000 charges wth only non-bonded interactions, and a real molecular model of more than 35,000 atoms with full atomic interactions, are used for the order-N and parallel scalability testing. An application to a liquid crystalline material will be discussed.
Citation:
Zhiqiang Wang, James Lupo, Alan McKenney, Ruth Pachter, "Large Scale Molecular Dynamics Simulations with Fast Multipole Implementations," sc, pp.56, Proceedings of the 1999 ACM/IEEE conference on Supercomputing, 1999
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