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Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit

文献类型：期刊论文

作者Liu, Li2,3; Liu, Xiaofeng2; Gong, Jiayu3; Jiang, Hualiang1,2; Li, Honglin2
刊名JOURNAL OF CHEMICAL THEORY AND COMPUTATION
出版日期2011-06
卷号7期号:6页码:1595-1603
ISSN号1549-9618
DOI10.1021/ct100728k
文献子类Article
英文摘要All-atom normal mode analysis (NMA) is an efficient way to predict the collective motions in a given macromolecule, which is essential for the understanding of protein biological function and drug design. However, the calculations are limited in time scale mainly because the required diagonalization of the Hessian matrix by Householder-QR transformation is a computationally exhausting task. In this paper, we demonstrate the parallel computing power of the graphics processing unit (GPU) in NMA by mapping Householder-QR transformation onto GPU using Compute Unified Device Architecture (CUDA). The results revealed that the GPU-accelerated all-atom NMA could reduce the runtime of diagonalization significantly and achieved over 20 x speedup over CPU-based NMA. In addition, we analyzed the influence of precision on both the performance and the accuracy of GPU. Although the performance of GPU with double precision is weaker than that with single precision in theory, more accurate results and an acceptable speedup of double precision were obtained in our approach by reducing the data transfer time to a minimum. Finally, the inherent drawbacks of GPU and the corresponding solution to deal with the limitation in computational scale are also discussed in this study.
WOS关键词GLUTAMINE-BINDING PROTEIN ; MOLECULAR-DYNAMICS ; FREE-ENERGY ; COMPLEXES ; MOTIONS ; CUDA ; FORM ; GPU ; IMPLEMENTATION ; ARCHITECTURES
资助项目Special Fund for Major State Basic Research Project[2009CB918501] ; Special Fund for Major State Basic Research Project[2011CB910200] ; National Natural Science Foundation of China[20803022] ; Shanghai Committee of Science and Technology[09dZ1975700] ; Shanghai Committee of Science and Technology[10431902600] ; Major National Scientific and Technological Project of China[2011ZX09307-002-03] ; Major National Scientific and Technological Project of China[2009ZX09501-001] ; Major National Scientific and Technological Project of China[2009ZX09301-001] ; Fundamental Research Funds for the Central Universities[00000000] ; Shanghai Rising-Star Program[10QA1401800] ; Program for New Century Excellent Talents in University[00000000] ; Chinese Academy of Sciences (CAS)[00000000]
WOS研究方向Chemistry ; Physics
语种英语
WOS记录号WOS:000291500400003
出版者AMER CHEMICAL SOC
源URL[http://119.78.100.183/handle/2S10ELR8/278514]  
专题药物发现与设计中心
通讯作者Li, Honglin
作者单位1.Chinese Acad Sci, Shanghai Inst Mat Med, Drug Discovery & Design Ctr, Shanghai 201203, Peoples R China
2.E China Univ Sci & Technol, State Key Lab Bioreactor Engn, Shanghai Key Lab Chem, Sch Pharm, Shanghai 200237, Peoples R China;
3.E China Univ Sci & Technol, Sch Informat Sci & Engn, Shanghai 200237, Peoples R China;
推荐引用方式
GB/T 7714		 Liu, Li,Liu, Xiaofeng,Gong, Jiayu,et al. Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit[J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION,2011,7(6):1595-1603.
APA Liu, Li,Liu, Xiaofeng,Gong, Jiayu,Jiang, Hualiang,&Li, Honglin.(2011).Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit.JOURNAL OF CHEMICAL THEORY AND COMPUTATION,7(6),1595-1603.
MLA Liu, Li,et al."Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit".JOURNAL OF CHEMICAL THEORY AND COMPUTATION 7.6(2011):1595-1603.

入库方式： OAI收割

来源：上海药物研究所

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