Development of the MD-GRAPE,a High-Speed Accelerator with a Parallel Processor Design for Molecular Dynamics Simulations, and its Application to Studies of Biological Membranes

分子动力学模拟并行处理器设计高速加速器MD-GRAPE的研制及其在生物膜研究中的应用

• 批准号: 04558036
• 负责人: KUSUMI Akihiko
• 金额: $ 13.12万
• 依托单位: The University of Tokyo
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Developmental Scientific Research (B)
• 财政年份: 1992
• 资助国家: 日本
• 起止时间: 1992 至 1993
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-04558036/
• 关键词: molecular dynamics simulations; super computer; special purpose computer; custom IC; LSI; protein; biological membrane; periodic boundary conditions; 分子動力学計算; AMBER

Because of its great computational complexity, the use of molecular dynamics (MD) simulations for studying large systems like those of biological macromolecules is severely limited by the availability of computer resources. As the size of the system of interest increases, the number of non-bonded forces (Coulombic and van der Waals interactions) to be calculated increases as O(N2), where N is the number of particles in the system. Cutoffs of Coulombic interactions cause various detrimental effects and should be avoided. The calculation of non-bonded forces consumes more than 99% of the CPU time in and MD simulation involving over 10,000 particles. To overcome this problem, we have developed a special-purpose parallel machine that is plugged into a workstation to accelerate the calculation of non-bonded interactions. The machine is a scalable homogeneous multiprocessor called an "MD Engine". Each processor element in the machine, an LSI chip of about 130,000 gates fabricated with 0.8mm CMOS standard-cell technology, has a pipeline architecture to calculate the total non-bonded force using the coordinates, electric charge, and species of each particle broadcast by the host computer. After the force is calculated, the processor sends it back to the host. The MD Engine also calculates virials simultaneously with forces for use in the calculation of pressure, accommodates periodic boundary conditions, and can be used in Ewald summations. The precision of arithmetic operations inside the processor is optimized, and the force is calculated with sufficient accuracy for practical MD simulations. MD simulation of a Ras p21 protein molecule immersed in a water sphere (11,940 particles) was accelerated by a factor of 75 using an MD Engine system consisting of 24 processors and plugged into a SPARCstation 10/51.

由于计算复杂度高，利用分子动力学（MD）模拟研究生物大分子等大型系统受到计算机资源的严重限制。随着感兴趣的系统的大小增加，要计算的非键力（库仑和范德华相互作用）的数量增加为O(N2)，其中N为系统中的粒子数。库仑相互作用的切断会造成各种不利影响，应避免。在涉及超过10,000个粒子的MD模拟中，非结合力的计算消耗了99%以上的CPU时间。为了克服这个问题，我们开发了一种特殊用途的并联机器，该机器插入工作站以加速非键合相互作用的计算。该机器是一个可扩展的同构多处理器，称为“MD引擎”。该机器中的每个处理器元件是一个由约13万个栅极组成的大规模集成电路芯片，采用0.8mm CMOS标准单元技术制造，具有流水线架构，可以使用主计算机广播的每个粒子的坐标、电荷和种类来计算总非键合力。计算出力后，处理器将其发送回主机。MD引擎还可以与力同时计算压力，适应周期性边界条件，并可用于Ewald求和。优化了处理器内部算术运算的精度，计算出的力具有足够的精度，可用于实际的MD仿真。使用由24个处理器组成并插入SPARCstation 10/51的MD Engine系统，将浸没在水球（11,940个粒子）中的Ras p21蛋白分子的MD模拟速度提高了75倍。

项目成果

T.Amisaki, T.Fujiwara,and A.Kusumi: "Error Evaluations for the Design of Special-Purpose Processor for Molecular Dynamics Simulations" J.Comp.Chem.(印刷中).

T. Amisaki、T. Fujiwara 和 A. Kusumi：“分子动力学模拟专用处理器设计的误差评估”J. Comp。

T.Amisaki, T.Fujiwara, A.Kusumi, H.Miyagawa, and K.Kitamura: "Error evaluation in the design of a special-purpose processor that calculates non-bonded forces in molecular dynamics simulations." J.Comp.Chem.(in press). (1995)

T.Amisaki、T.Fujiwara、A.Kusumi、H.Miyakawa 和 K.Kitamura：“计算分子动力学模拟中非键合力的专用处理器设计中的错误评估。”

T.Amisaki,T.Fujiwara,and A.Kusumi: "Error Evaluations for the Design of Special-Purpose Processor for Molecular Dynamics Simulations" Molecular Simulation. (印刷中).

T. Amisaki、T. Fujiwara 和 A. Kusumi：“分子动力学模拟专用处理器设计的误差评估”分子模拟（正在出版）。