Development of high performance computation system with great precision for molecular dynamics simulations
| Project/Area Number |
10680636
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Biophysics
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| Research Institution | Shimane University |
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Principal Investigator |
AMISAKI Takashi Shimane University, Faculty of Science and Engineering, Associate Professor, 総合理工学部, 助教授 (20231996)
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| Project Period (FY) |
1998 – 1999
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| Project Status |
Completed (Fiscal Year 1999)
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| Budget Amount *help |
¥3,400,000 (Direct Cost: ¥3,400,000)
Fiscal Year 1999: ¥1,200,000 (Direct Cost: ¥1,200,000)
Fiscal Year 1998: ¥2,200,000 (Direct Cost: ¥2,200,000)
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| Keywords | molecular dynamics / hardware / algorithm / fast multipole method / Ewald method / computation system / accuracy / parallel processing / 専用計算機 / バルク同期並列 / メッセージ通信 |
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| Research Abstract |
Molecular dynamics simulation provides valuable means to study the structure and dynamics of molecular systems. Since it demands vast computational resources, particularly when it is applied to large biological systems, it presents challenging problems to computational technology. Although several fast algorithms were developed for reducing the computation time, these algorithms encounter certain difficulties. In this work, I first reformulated the fast multipole method (FMM) for further decreasing the computation time and memory requirements. Secondly, I developed two reliable algorithms for accomplishing periodicity in the FMM framework. One method employs the Ewald-like technique, and the other uses a macroscopic hierarchical structure of cells. These methods developed in this work enable reliable simulations of biological macromolecules.
Since every fast algorithm including FMM employs a certain kind of approximation, the algorithms suffer from inaccuracy in some situation. In this work, I found that use of a special-purpose machine for a task involved in FMM improve both accuracy and computation speed. Such a computation system with novel algorithms was actually developed in this work. The performance of the system was confirmed to be several hundred times higher than those of ordinary workstations.
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Report
(3 results)
Research Products
(2 results)
