Large Scale Biomolecular Dynamics Simulations - prace

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GROMACS • The world’s fastest MD code - and it’s GPL! • Estimated 5,000-10,000 academic and industrial users • Used in Folding@Home - 250,000 CPUs (2008) • Part of SPECfp & PRACE benchmark suites • PRACE project for improvements on GROMACS (CSC, Erik Lindahl) onsdag, 2009 maj 13
DPPC & Cholesterol: 130k atoms BlueGene: 6ns/day, using 2000 CPUs GROMACS only achieves 2ns/day ... ...on a single dual dual core Opteron node! onsdag, 2009 maj 13
Page 1 and 2: XXL-BIOMD Large Scale Biomolecular
Page 3 and 4: Protein BBA5: 4000 Waters: Total: 4
Page 5 and 6: BBA5 folding: CPU Time • 12400 at
Page 7: Simulation vs. Experiments Experime
Page 11 and 12: The Eighth-Sphere Method • Smarte
Page 13 and 14: Scaling - DHFR 23558 atoms
Page 15 and 16: Deisa Extreme Computing Initiative
Page 17 and 18: Why study viruses? • New viral di
Page 19 and 20: 5 ns simulation. Blue: protein. Gre
Page 21 and 22: onsdag, 2009 maj 13
Page 23 and 24: The goal is not merely reproducing
Page 25 and 26: Simulation Details • 1,000,000+ p
Page 27 and 28: Superposition of 60 monomers after
Page 29 and 30: onsdag, 2009 maj 13 Size of the vir
Page 31 and 32: onsdag, 2009 maj 13 Physiological C
Page 33 and 34: Questions & future plans... • Wha
Page 35: Molecular Biophysics, Uppsala Danie

Large Scale Biomolecular Dynamics Simulations - prace

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