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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 report on resent astrophysical N-body simulations performed on the GRAPE-4 (GRAvity PipE 4) system, a special-purpose computer for astrophysical N-body simulations. We first review the astrophysical motivation, the algorithm, the structure of the GRAPE system, and the actual performance. The GRAPE-4 system consists of 1692 pipeline processors. The peak(More)
We describe the GRAPE-4 (Gravity Pipe 4) system, a special-purpose computer for astrophysical N-body simulations. In N-body simulations, most of the computing time is spent to calculate the force between particles, since the number of interactions is proportional to the square of the number of particles. For many problems the accuracy of fast algorithms(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)
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)