Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program

Authors:
Michael Crowley;Tom Darden;Thomas Cheatham, III;David Deerfield, II
Affiliations:
Pittsburgh Supercomputing Center, 4400 Fifth Avenue, Pittsburgh, PA 15213 crowley@psc.edu;National Institutes of Environmental Health Sciences, Research Triangle Park, North Carolina 27709 darden@niehs.nih.gov;NIH Campus Bldg 12A,9000 Rockville Pike, Bethesda MD 20892 cheatham@helix.nih.gov;Pittsburgh Supercomputing Center, 4400 Fifth Avenue, Pittsburgh, PA 15213 deerfiel@psc.edu
Venue:
The Journal of Supercomputing - Special issue on supercomputing in medicine
Year:
1997

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Abstract

We report our work to parallelize the Particle Mesh Ewald (PME) methodto compute the long-range electrostatic interactions in the moleculardynamics program AMBER and to extend the scalability of the PME methodto hundreds of processors.