Fast algorithm/ hardware joint acceleration for molecular dynamics simulations and its efficacy confirmation

分子动力学模拟快速算法/硬件联合加速及其有效性验证

• 批准号: 13680743
• 负责人: AMISAKI Takashi
• 金额: $ 2.24万
• 依托单位: Tottori University
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (C)
• 财政年份: 2001
• 资助国家: 日本
• 起止时间: 2001 至 2002
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-13680743/
• 关键词: molecular dynamics; proteins; fast multipole methods; special-purpose machine; parallel computing; cluster computing; computation accuracy; MD-Engine; SHAKE; 専用ハードウェア

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.To overcome this problem, in this work, I developed algorithms that realized efficient cooperation of dedicated computational board (MD-Engine II) with fast algorithms, such as fast multipole method (FMM). The algorithms were implemented on a PC, into which the computation boards were plugged, to acutally build up a specialized computation unit for MD simulations. I then developed a cluster of the four computation units to realize a high performace system for accurate MD calculation at low cost. Using the computation system, 1MD step of a protein-water system (fifty thousand atoms) can be completed in 1.6s. In addition, the results of a series of 50 ps MD simulations of a protein-water system (fifty thousand atoms) revealed that a more stringent setting of accuracy in FMM computation, as compared with those previously reported, was required for accurate simulations over long time periods.

分子动力学模拟为研究分子系统的结构和动力学提供了有价值的手段。由于它需要大量的计算资源，特别是当它被应用到大型生物系统，它提出了具有挑战性的问题，计算技术。为了解决这一问题，本文提出了一种新的快速算法，实现了专用计算板（MD-Engine II）与快速多极子方法（FMM）等快速算法的有效协作。这些算法在PC机上实现，并将计算板插入PC机，从而真正构成了MD模拟的专用计算单元。然后，我开发了一个集群的四个计算单元，以实现一个高性能的系统，准确的MD计算在低成本。利用该计算系统，蛋白质-水体系（5万个原子）的1 MD步骤可以在1.6s内完成。此外，一系列50 ps的蛋白质-水系统（5万个原子）的MD模拟的结果表明，与以前报道的相比，在FMM计算中需要更严格的精度设置，才能长时间精确模拟。

项目成果

T,Amisaki., S,Toyoda., H,Miyagawa., K,Kitamura.: "Two algorithms designed for realizing efficient combination of fast multipole method and dedicated hardware for molecular dynamics simulations"J. Computer Chemistry, Japan. 1, No.3. 73-82 (2002)

T,Amisaki., S,Toyoda., H,Miyakawa., K,Kitamura.：“为实现快速多极方法和分子动力学模拟专用硬件的有效组合而设计的两种算法”J.

H,Takashima., T,Amisaki., K,Kitamura., U,Nagashima.: "Numerical accuracy on Fm(z) for molecular integral calculations"Computer Physics Communications. 148, No.2. 182-187 (2002)

H，Takashima.，T，Amisaki.，K，Kitamura.，U，Nagashima.：“分子积分计算中 Fm(z) 的数值精度”计算机物理通讯。

網崎孝志: "高速多重極法と専用計算機の併用による分子動力学計算高速化のための二つのアルゴリズム"J.Computer Chemistry, Japan. 1・3. 73-82 (2002)

Takashi Amizaki：“通过结合快速多极方法和专用计算机来加速分子动力学计算的两种算法”J.Computer Chemistry，日本 1・3（2002）。