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The parallel operation of computer is carried out using PC and DEC workstation. Combining the molecular dynamics simulation , the parallel efficiency and computational result are analyzed through a great deal of experiments. At the same time, the high temperature- induced denaturalization of protein GB1 is studied using the software of parallel molecular dynamic simulation. 利用PC和DEC工作站实现了计算机并行计算,结合生物信息学中的分子动力学模拟,对并行效率和计算结果进行了大量实验分析,同时用并行的分子动力学模拟软件对GB1蛋白质高温变性进行了简单分析. This paper presents a "Block Cell Link" parallel molecular dynamics method, which included a dynamic load balancing algorithm based on HSFC.It implements the scalable parallel computing based on MPI for large scale, non uniform molecular dynamic simulation. It helps physicists fulfill nano meter scale simulating compared with observed data. Both simulating 380 millions 2D particles and simulating 276 millions 3D particles have achieved speedup above 209 with 240 processors on a MPP machine. 提出一种基于“块 单元 链表”数据结构和HSFC动态负载平衡的并行分子动力学算法 ,实现了大规模、非均匀分子动力学模拟的基于MPI的可扩展并行计算 ,以辅助物理学家实现具有实验意义的纳米级模拟。具体地 ,在某MPP并行机的 2 4 0个CPU上 ,计算 3 84亿 (二维 )和 2 76亿 (三维 )个粒子规模的金属微喷射问题 ,均获得了 2 0 9倍以上的加速比。 Aimed at the defect of small simulation model,slow calculating speed of molecular dynamics simulation technique,a new technique of parallel programming simulation of molecular dynamics was put forward.This technique combines parallel programming with the computer simulation of molecular dynamics.It can largen the model,improve the speed,make the model much more close to the reality,and can accelerate the research of ultraprecision manufacturing microcosmic mechanism. 在精密加工中应用分子动力学仿真技术,存在仿真模型较小、计算速度太慢等问题,为此提出了并行分子动力学仿真技术,它是在原来的分子动力学仿真技术里面加入并行的思想,用并行的优势来弱化原仿真的劣势,可以扩大仿真规模,提高运算速度,使仿真模型更加接近于实际,从而促进超精密加工微观机理的研究。
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