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As an entry for the 2009 Gordon Bell price/performance prize, we present the results of two different hierarchical N-body simulations on a cluster of 256 graphics processing units (GPUs). Unlike many previous N-body simulations on GPUs that scale as O(N 2), the present method calculates the O(N log N) treecode and O(N) fast multipole method (FMM) on the(More)
We performed molecular dynamics (MD) simulation of 9 million pairs of NaCl ions with the Ewald summation and obtained a calculation speed of 1.34 Tflops. In this calculation we used a special-purpose computer, MDM, which we are developing for the calculations of the Coulomb and van der Waals forces. The MDM enabled us to perform large-scale MD simulations(More)
1 We have achieved a sustained performance of 55 TFLOPS for molecular dynamics simulations of the amyloid fibril formation of peptides from the yeast Sup35 in an aqueous solution. For performing the calculations, we used the MDGRAPE-3 system—a special-purpose computer system for molecular dynamics simulations. Its nominal peak performance was 415 TFLOPS for(More)
We are developing the 'Protein Explorer' system, a petaflops special-purpose computer system for molecular dynamics simulations. The Protein Explorer is a PC cluster equipped with special-purpose engines that calculate nonbonded interactions between atoms, which is the most time-consuming part of the simulations. A dedicated LSI 'MDGRAPE-3 chip' performs(More)
—We present a 0.5 Petaflop/s calculation of homogeneous isotropic turbulence in a cube of 2048 3 particles, using a highly parallel fast multipole method (FMM) using 2048 GPUs on the TSUBAME 2.0 system. We compare this particle-based code with a spectral DNS code under the same calculation condition and the same machine. The results of our particle-based(More)
Virtual compound screening using molecular docking is widely used in the discovery of new lead compounds for drug design. However, this method is not completely reliable and therefore unsatisfactory. In this study, we used massive molecular dynamics simulations of protein-ligand conformations obtained by molecular docking in order to improve the enrichment(More)
Scientific applications do frequently suffer from limited compute performance. In this article, we investigate the suitability of specialized computer chips to overcome this limitation. An enhanced Poisson Boltzmann program is ported to the graphics processing unit and the application specific integrated circuit MDGRAPE-3 and resulting execution times are(More)