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)
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 have achieved a sustained calculation speed of 281 Tflops for the optimization of the 3-D structures of proteins from the X-ray experimental data by the Genetic Algorithm - Direct Space (GA-DS) method. In this calculation we used MDGRAPE-3, special-purpose computer for molecular simulations, with the peak performance of 752 Tflops. In the GA-DS method, a… (More)
PetaFLOPS computers---capable of performing a thousand trillion mathematical operations per second, 25 times faster than the largest supercomputers today---will open new doors to understanding the functions of biological molecules.