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

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 these force calculations at a speed of 165 gigaflops or higher. The system will have 6,144 MDGRAPE-3 chips to achieve a nominal peak performance of one petaflop. The system will be completed in 2006. In this paper, we describe the project plans and the architecture of the Protein Explorer.

[1]  Toshiyuki Fukushige,et al.  A 29.5 Tflops Simulation of Planetesimals in Uranus-Neptune Region on GRAPE-6 , 2002, ACM/IEEE SC 2002 Conference (SC'02).

[2]  A. F. Bakker,et al.  Design and implementation of the Delft molecular dynamics processor , 1988 .

[3]  Toshikazu Ebisuzaki,et al.  A Special-Purpose Computer for N-Body Simulations:GRAPE-2A (GRAPE) , 1993 .

[4]  Makoto Taiji,et al.  Scientific simulations with special purpose computers - the GRAPE systems , 1998 .

[5]  Toshikazu Ebisuzaki,et al.  GRAPE-4: a teraFLOPS massively parallel special-purpose computer system for astrophysical N-body simulations , 1994, Proceedings of 8th International Parallel Processing Symposium.

[6]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[7]  M. Parrinello,et al.  Polymorphic transitions in single crystals: A new molecular dynamics method , 1981 .

[8]  Toshikazu Ebisuzaki,et al.  A special-purpose computer for gravitational many-body problems , 1990, Nature.

[9]  Junichiro Makino,et al.  Treecode with a Special-Purpose Processor , 1991 .

[10]  J. Makino,et al.  HARP--A Special-Purpose Computer for N-Body Problem (GRAPE) , 1993 .

[11]  Toshiyuki Fukushige,et al.  GRAPE-6: Massively-Parallel Special-Purpose Computer for Astrophysical Particle Simulations , 2003, astro-ph/0310702.

[12]  T. Ebisuzaki,et al.  Molecular Dynamics Machine: Special-Purpose Computer for Molecular Dynamics Simulations , 1999 .

[13]  Akihiko Konagaya,et al.  Molecular dynamics, free energy, and SPR analyses of the interactions between the SH2 domain of Grb2 and ErbB phosphotyrosyl peptides. , 2003, Biochemistry.

[14]  Toshikazu Ebisuzaki,et al.  Performance Analysis of High-Accuracy Tree Code Based on the Pseudoparticle Multipole Method , 2004 .

[15]  Toshikazu Ebisuzaki,et al.  A Highly Parallelized Special-Purpose Computer for Many-Body Simulations with an Arbitrary Central Force: MD-GRAPE , 1996 .

[16]  Toshikazu Ebisuzaki,et al.  A special purpose computer for particle dynamics simulation based on Ewald method: WINE-1 , 1993, [1993] Proceedings of the Twenty-sixth Hawaii International Conference on System Sciences.

[17]  T. Koishi,et al.  An 8.61 Tflop/s Molecular Dynamics Simulation for NaCl with a Special-Purpose Computer: MDM , 2000, ACM/IEEE SC 2001 Conference (SC'01).

[18]  Atsushi Kawai,et al.  Pseudoparticle Multipole Method: A Simple Method to Implement a High-Accuracy Tree Code , 2000, astro-ph/0012041.

[19]  Alan H. Karp.  Speeding up N-body Calculations on Machines without Hardware Square Root , 1992, Sci. Program..

[20]  R Fine,et al.  FASTRUN: A special purpose, hardwired computer for molecular simulation , 1991, Proteins.

[21]  Toshikazu Ebisuzaki,et al.  Molecular Dynamics Simulations of Prion Proteins-Effect of Ala117 .RAR.Val mutation- , 2003 .

[22]  Toshikazu Ebisuzaki,et al.  1.34 Tflops Molecular Dynamics Simulation for NaCl with a Special-Purpose Computer: MDM , 2000, ACM/IEEE SC 2000 Conference (SC'00).

[23]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .