MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations

MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations

We are developing the MDGRAPE-4, a special-purpose computer system for molecular dynamics (MD) simulations. MDGRAPE-4 is designed to achieve strong scalability for protein MD simulations through the integration of general-purpose cores, dedicated pipelines, memory banks and network interfaces (NIFs) to create a system on chip (SoC). Each SoC has 64 dedicated pipelines that are used for non-bond...

A special purpose computer for ab initio molecular dynamics simulations

Parallelized Simulation of Molecular Dynamics with a Special-Purpose Computer: MDGRAPE-2

1 High Performance Biocomputing Research Team, Bioinformatics Group, Genomic Sciences Center, RIKEN, 61-1 Onocho, Tsurumi, Yokohama, Kanagawa 230-0046, Japan 2 Computational Science Division, Advanced Computing Center, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan 3 Saitama Institute of Technology, 1690 Husaiji, Okabemachi, Osatogun, Saitama 3690293, Japan 4 Department of Mechanical Engine...

Protein Explorer: A Petaflops Special-Purpose Computer for Molecular Dynamics Simulations

Molecular dynamics (MD) simulation is one of the most exact and powerful method to study protein biophysics and biochemistry. However, its use is still limited by its high requirement of computational power. To solve this problem, several special-purpose computers have been built. The most successful machines are GRAPE family [1], GRAPE-2A, MD-GRAPE, and MDM. Especially, MDM [2] with 78 teraflo...

A high performance system for molecular dynamics simulation of biomolecules using a special-purpose computer.

GRAPE (GRavity PipE) processors are special purpose computers for simulation of classical particles. The performance of MD-GRAPE, one of the GRAPEs developed for molecular dynamics, was investigated. The effective speed of MD-GRAPE was equivalent to approximately 6 Gflops. The precision of MD-GRAPE was good judging from the acceptable fluctuation of the total energy. Then a software named PEACH...