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» Large Scale Simulation of Parallel Molecular Dynamics
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IPPS
2006
IEEE
14 years 1 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...
ICS
2009
Tsinghua U.
14 years 1 months ago
Dynamic topology aware load balancing algorithms for molecular dynamics applications
Molecular Dynamics applications enhance our understanding of biological phenomena through bio-molecular simulations. Large-scale parallelization of MD simulations is challenging b...
Abhinav Bhatele, Laxmikant V. Kalé, Sameer ...
ASAP
2009
IEEE
142views Hardware» more  ASAP 2009»
14 years 4 months ago
Parallel Discrete Event Simulation of Molecular Dynamics Through Event-Based Decomposition
—Molecular dynamics simulation based on discrete event simulation (DMD) is emerging as an alternative to time-step driven molecular dynamics (MD). DMD uses simplified discretize...
Martin C. Herbordt, Md. Ashfaquzzaman Khan, Tony D...
CCGRID
2007
IEEE
13 years 11 months ago
Large Scale Deployment of Molecular Docking Application on Computational Grid infrastructures for Combating Malaria
Computational grids are solutions for several biological applications like virtual screening or molecular dynamics where large amounts of computing power and storage are required....
Vinod Kasam, Jean Salzemann, Nicolas Jacq, Astrid ...
WSC
1998
13 years 8 months ago
Parallel Implementation of a Molecular Dynamics Simulation Program
We have taken a NIST molecular dynamics simulation program (md3), which was configured as a single sequential process running on a CRAY C90 vector supercomputer, and parallelized ...
Alan Mink, Christophe Bailly