Pairwise fragment interaction computation

Details Pairwise fragment interaction computation Pairwise fragment interaction computation

2007-10-29

2011-11-22

Sims, Jason (Department: 1631)

Data processing: measuring, calibrating, or testing

Measurement system in a specific environment

Biological or biochemical

C703S019000

Reexamination Certificate

active

08065090

ABSTRACT:
A method for creating a load balanced spatial partitioning of a structured, diffusing system of particles with pairwise interactions includes steps of: assigning a weight corresponding to a computational cost for a pair interaction of particles to a simulation space distance between the particles; performing a spatial partitioning of the simulation space; and assigning computation of pair interaction to any node that has the positions of both particles.

REFERENCES:
Nyland et al., Achieving Scalable parallel Molecular Dynamics Using Dynamic Spatial Domain Decomposition Techniques, 1997, Journal of Parallel and Distributed Computing, vol. 47, pp. 125-138.
Nakano, Aiichiro, Multiresolution Load Balancing in Curved Space: the wavelet representation, 1999, Concurrency: Practice and Experience, vol. 11, pp. 343-353.
IBM Blue Gene team, “Blue Gene: A vision for protein science using a petaflop supercomputer.” 2001.
T. P. Straatsma, J. A. McCammon, “Load balancing of molecular dynamics simulation with NWChem.” 2201.
The BlueGene/L Team, “An overview of the BlueGene/L supercomputer.” 2002.

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