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Development of hardware accelerator for molecular dynamics simulations: A computation board that calculates nonbonded interactions in cooperation with fast multipole method
Author(s) -
Amisaki Takashi,
Toyoda Shinjiro,
Miyagawa Hiroh,
Kitamura Kunihiro
Publication year - 2003
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.10193
Subject(s) - computation , bottleneck , multipole expansion , fast multipole method , computer science , molecular dynamics , computational science , parallel computing , range (aeronautics) , speedup , pairwise comparison , algorithm , chemistry , physics , computational chemistry , engineering , embedded system , aerospace engineering , artificial intelligence , quantum mechanics
Evaluation of long‐range Coulombic interactions still represents a bottleneck in the molecular dynamics (MD) simulations of biological macromolecules. Despite the advent of sophisticated fast algorithms, such as the fast multipole method (FMM), accurate simulations still demand a great amount of computation time due to the accuracy/speed trade‐off inherently involved in these algorithms. Unless higher order multipole expansions, which are extremely expensive to evaluate, are employed, a large amount of the execution time is still spent in directly calculating particle–particle interactions within the nearby region of each particle. To reduce this execution time for pair interactions, we developed a computation unit (board), called MD‐Engine II, that calculates nonbonded pairwise interactions using a specially designed hardware. Four custom arithmetic‐processors and a processor for memory manipulation (“particle processor”) are mounted on the computation board. The arithmetic processors are responsible for calculation of the pair interactions. The particle processor plays a central role in realizing efficient cooperation with the FMM. The results of a series of 50‐ps MD simulations of a protein–water system (50,764 atoms) indicated that a more stringent setting of accuracy in FMM computation, compared with those previously reported, was required for accurate simulations over long time periods. Such a level of accuracy was efficiently achieved using the cooperative calculations of the FMM and MD‐Engine II. On an Alpha 21264 PC, the FMM computation at a moderate but tolerable level of accuracy was accelerated by a factor of 16.0 using three boards. At a high level of accuracy, the cooperative calculation achieved a 22.7‐fold acceleration over the corresponding conventional FMM calculation. In the cooperative calculations of the FMM and MD‐Engine II, it was possible to achieve more accurate computation at a comparable execution time by incorporating larger nearby regions. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 582–592, 2003