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Application of a high‐performance, special‐purpose computer, GRAPE‐2A, to molecular dynamics
Author(s) -
Higo Junichi,
Endo Shigeru,
Nagayama Kuniaki,
Ito Tomoyoshi,
Fukushige Toshiyuki,
Ebisuzaki Toshikazu,
Sugimoto Daiichiro,
Miyagawa Hiroo,
Kitamura Kunihiro,
Makino Junichiro
Publication year - 1994
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540151207
Subject(s) - pairwise comparison , workstation , host (biology) , computer science , molecular dynamics , dynamics (music) , computational science , chemistry , physics , operating system , computational chemistry , artificial intelligence , ecology , acoustics , biology
The special‐purpose computer GRAPE‐2A accelerates the calculation of pairwise interactions in many‐body systems. This computer is a back‐end processor connected to a host computer through a Versa Module Europe (VME) bus. GRAPE‐2A receives coordinates and other physical data for particles from the host and then calculates the pairwise interactions. The host then integrates an equation of motion by using these interactions. We did molecular dynamics simulations for two systems of liquid water: System 1 (1000 molecules), and System 2 (1728 molecules). The time spent for one step of molecular dynamics was 3.9 s (System l), and 10.2 s (System 2). The larger the molecular system, the higher the performance. The speed of GRAPE‐2A did not depend on the formula describing the pairwise interaction. The cost performance was about 20 times better than that of the fastest workstations available today, and GRAPE‐2A cost only $22,000. © 1994 by John Wiley & Sons, Inc.