Development of hardware accelerator for molecular dynamics simulations: A computation board that calculates nonbonded interactions in cooperation with fast multipole method
✍ Scribed by Takashi Amisaki; Shinjiro Toyoda; Hiroh Miyagawa; Kunihiro Kitamura
- Publisher
- John Wiley and Sons
- Year
- 2003
- Tongue
- English
- Weight
- 302 KB
- Volume
- 24
- Category
- Article
- ISSN
- 0192-8651
No coin nor oath required. For personal study only.
✦ Synopsis
Abstract
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