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J4 ›› 2012, Vol. 47 ›› Issue (7): 14-19.

• 生命科学 • 上一篇    下一篇

生物大分子的分子动力学模拟过程在百万亿次集群上的部署优化

潘龙强1,2,耿存亮1,慕宇光3,刘鑫4,胡毅5,潘景山4,周亚滨2,龚斌5,王禄山1*   

  1. 1.山东大学微生物技术国家重点实验室, 山东 济南 250100; 2.山东大学病原生物学研究所, 山东 济南 250012;
    3.南洋理工大学生命科学学院, 新加坡(新加坡) 637551; 4.国家超算济南中心, 山东 济南 250101;
    5.山东大学计算机科学与技术学院, 山东 济南 250101
  • 收稿日期:2012-03-08 出版日期:2012-07-20 发布日期:2012-09-01
  • 通讯作者: 王禄山(1974- ),男,副教授,硕士生导师,研究方向为微生物生理生化及生物信息学. Email:lswang@sdu.edu.cn
  • 作者简介:潘龙强(1988- ),男,硕士研究生,研究方向为分子病毒学及其生物信息学. Email:plq@mail.sdu.edu.cn
  • 基金资助:

    973计划资助项目(2011CB707401);国家自然科学基金资助项目(31070063);山东省优秀中青年奖励基金项目(20090451326)

Deployment and optimization of biomacromolecule molecular dynamics simulation process on hundred trillion times cluster

PAN Long-qiang1,2, GENG Cun-liang1, MU Yu-guang3, LIU Xin4, HU Yi5, PAN Jing-shan4, ZHOU Ya-bin2, GONG Bin5, WANG Lu-shan1*   

  1. 1. The State Key Laboratory of Microbial Technology Shandong University, Jinan 250100, Shandong, China;
    2. Department of Pathogenic Biology, Shandong University School of Medicine, Jinan 250012, Shandong, China;
    3. School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore;
    4. National Supercomputing Center in Jinan, Jinan 250101, Shandong, China;
    5. School of Computer Science and Technology, Shandong University, Jinan 250101, Shandong, China
  • Received:2012-03-08 Online:2012-07-20 Published:2012-09-01

摘要:

分子动力学模拟作为研究生物大分子功能和性质的新工具,已广泛应用于蛋白质和核酸等物质的分子动态学行为研究,但目前常规分子动力学模拟时间尺度较小,不能达到生物大分子分子动态行为的有效取样范围。温度副本交换分子动力学可同时运行多个独立模拟,明显提高模拟时间的可及尺度,但需要千核以至万核的计算资源,目前已发表的相关文献其模拟体系使用的计算资源均较小。本文利用国家超算济南中心的神威4000A百万亿次集群,首先进行单副本的分子动力学模拟,然后利用外切纤维素酶催化结构域的模拟体系(约5万原子)进行多达128个温度副本的分子动力学模拟,一次模拟任务最多成功利用6720个CPU核心同时进行计算,最高总运算速度累计达到2274ns/d,这为分子动力学模拟利用上万核心进行计算提供了新的思路。

关键词: 分子动力学模拟;副本交换;百万亿次;神威4000A;部署优化

Abstract:

As a novel tool to study the functions and properties of biomacromolecules, molecular dynamics has been extensively used to investigate the molecular dynamic behavior of proteins and nucleic acids. However, the time scale range of normal molecular dynamics simulation remains relatively narrow,which cannot reach the valid sampling range of biomacromolecules dynamics behavior recently. Temperature replica exchange molecular dynamics can run multiple independent simulations synchronously and effectively increase the simulating speed. Meanwhile, it requires tens of thousands of cores in aspect of the computing resources, yet the simulation systems of published literatures cannot reach such large scale hitherto. By using the 100T Flops cluster of sunway 4000A in National Supercomputing Center in Jinan, we firstly ran the molecular dynamics of single replica and then ran as many as 128 temperature replicas exchange molecular dynamics to simulate the catalytic domain of exocellulases (about 50000 atoms). We simultaneously used up to 6720 CPU cores in this task, the total computing speed accumulated to 2274ns/d, which offers a new approach to run the molecular dynamics over ten thousand CPU cores.

Key words: molecular dynamics simulation; replica exchange; hundred trillion times; Sunway 4000A; deployment and optimization

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