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CODES
2005
IEEE
13 years 9 months ago
Blue matter on blue gene/L: massively parallel computation for biomolecular simulation
This paper provides an overview of the Blue Matter application development effort within the Blue Gene project that supports our scientific simulation efforts in the areas of pro...
Robert S. Germain, Blake G. Fitch, Aleksandr Raysh...
IPPS
2008
IEEE
13 years 10 months ago
Overcoming scaling challenges in biomolecular simulations across multiple platforms
NAMD† is a portable parallel application for biomolecular simulations. NAMD pioneered the use of hybrid spatial and force decomposition, a technique now used by most scalable pr...
Abhinav Bhatele, Sameer Kumar, Chao Mei, James C. ...
IPPS
2006
IEEE
13 years 9 months ago
Parallel implementation of the replica exchange molecular dynamics algorithm on Blue Gene/L
The Replica Exchange method is a popular approach for studying the folding thermodynamics of small to modest size proteins in explicit solvent, since it is easily parallelized. Ho...
Maria Eleftheriou, Aleksandr Rayshubskiy, Jed W. P...
PPOPP
2006
ACM
13 years 9 months ago
Performance characterization of molecular dynamics techniques for biomolecular simulations
Large-scale simulations and computational modeling using molecular dynamics (MD) continues to make significant impacts in the field of biology. It is well known that simulations...
Sadaf R. Alam, Jeffrey S. Vetter, Pratul K. Agarwa...
IJHPCA
2008
96views more  IJHPCA 2008»
13 years 3 months ago
BlueGene/L applications: Parallelism On a Massive Scale
pc.sagepub.com/cgi/content/abstract/22/1/33 The online version of this article can be found at: Published by: http://www.sagepublications.com can be found at:International Journal ...
Bronis R. de Supinski, Martin Schulz, Vasily Bulat...