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 teraflops is still keeping the fastest computer in the world since 2000. Based on these success, we have started a project to build a special-purpose computer with petaflops performance, ‘Protein Explorer’. It will become the first petaflops machine in the world. The scientific targets are the prediction of affinity of (mutated) proteins and simulations of huge biomolecules to clarify its functions and mechanisms. The petaflops dedicated machine will give great contributions to bioscience.