MDGRAPE (Molecular Dynamics GRAvity PipE)
Oct. 31, 2006
Tetsu Narumi, RIKEN
narumi @ gsc.riken.go.jp

MDGRAPE is a special-purpose computer for molecular dynamics (MD) simulations. MD-GRAPE1,2 is the first machine developed in University of Tokyo. MDGRAPE-23 was developed in RIKEN, and commercially available. A big machine, Molecular Dynamics Machine (MDM)4,5, with a 78-Tflops peak performance was also developed with MDGRAPE-2 and WINE-26. MDGRAPE-37 is shipped from 2005.

MDGRAPE-3 MDGRAPE-3 hardware and library ( memo to use MDGRAPE-3 in Japanese and in English )
MDM Hardware of MDM, library for MDGRAPE-2, etc.
AMBER8 with MDGRAPE-2 How to use AMBER8 with MDGRAPE-2

1 Taiji, M., Fukushige, T., Makino, J., Ebisuzaki, T., and Sugimoto, D., "MD-GRAPE: A Parallel Special-Purpose Computer System for Classical Molecular Dynamics Simulations", Physics Computing '94 Lugano, Switzerland, in Proceedings of the 6th Joint EPS-APS international conference on Physics Computing, European Physical Society, Geneva, pp. 200-203, 1994.
2 Fukushige, T., Taiji, M., Makino, J., Ebisuzaki, T., and Sugimoto, D., "A Highly-Parallelized Special-Purpose Computer for Many-body Simulations with An Arbitrary Central Force: MD-GRAPE", Astrophysical Journal, 468, pp. 51-61, 1996.
3 Susukita R, Ebisuzaki T, Elmegreen BG, Furusawa H, Kato K, Kawai A, Kobayashi Y, Koishi T, McNiven GD, Narumi T, Yasuoka K, "Hardware accelerator for molecular dynamics: MDGRAPE-2", Computer Physics Communications, 155 (2), pp. 115-131, 2003.
4 Tetsu Narumi, Ryutaro Susukita, Toshikazu Ebisuzaki, Geoffrey McNiven, Bruce Elmegreen, "Molecular dynamics machine: Special-purpose computer for molecular dynamics simulations", Molecular Simulation, vol. 21, pp. 401-415, 1999.
5 Narumi T, "A special-purpose computer for molecular dynamics simulations: MDM", Astrophysical Supercomputing Using Particle Simulations, IAU Symposium (208), pp. 349-358, 2003.
6 Tetsu Narumi, Ryutaro Susukita, Hideaki Furusawa and Toshikazu Ebisuzaki, "46 Tflops Special-purpose Computer for Molecular Dynamics Simulations: WINE-2", in Proceedings of the 5th International Conference on Signal Processing, pp. 575-582, Beijing, 2000.
7 Taiji Makoto, Narumi Tetsu, Ohno Yousuke, Futatsugi Noriyuki, Suenaga Atsushi, Takada Naoki, Konagaya Akihiko, "Protein explorer: A petaflops special-purpose computer system for molecular dynamics simulations", in Proceedings of the SC2003 Technical Papers, CDROM, Phoenix, 2003.