MDGRAPE-3

A Petaflops special-purpose computer for molecular dynamics simulations

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What is MDGRAPE-3?: We are developing MDGRAPE-3 (aka `Protein Explorer'), a petaflops special-purpose computer system for molecular dynamics simulations of proteins and the other biomolecules/complexes. It will become the first Petaflops machine in the world when it will be finished in 2006. This project is a part of `Protein 3000 project', supported by Ministry of Education, Culture, Sports, Science and Technology of Japan.

Molecular dynamics simulation is one of the most important method to study physical, chemical and biological properties of materials in atomic level. In this method, the Newton's equations of motion are solved to integrate the orbits of the atoms. In this method, the most of computational time is spent for calculation of the forces between atoms, especially non-bonded forces (Coulomb and van der Waals forces). Therefore, a high-performance special-purpose computer to calculate non-bonded forces is very effective to accelerate simulations.