Accelerating Molecular Dynamic Simulation on Graphics Processing Units

被引：404

作者：

Friedrichs, Mark S. ^{[1
]}

Eastman, Peter ^{[1
]}

Vaidyanathan, Vishal ^{[2
]}

Houston, Mike ^{[3
]}

Legrand, Scott ^{[4
]}

Beberg, Adam L. ^{[5
]}

Ensign, Daniel L. ^{[2
]}

Bruns, Christopher M. ^{[1
]}

Pande, Vijay S. ^{[2
,5
]}

机构：

[1] Stanford Univ, Dept Bioengn, Stanford, CA 94305 USA

[2] Stanford Univ, Dept Chem, Stanford, CA 94305 USA

[3] Adv Micro Devices Inc, Sunnyvale, CA USA

[4] NVIDIA Corp, Santa Clara, CA USA

[5] Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA

来源：

JOURNAL OF COMPUTATIONAL CHEMISTRY | 2009年 / 30卷 / 06期

关键词：

GPU; molecular dynamics; implicit solvent; LAMBDA-REPRESSOR;

D O I：

10.1002/jcc.21209

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

We describe it complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU). including all standard force field terms, integration. constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance. and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core. (C) 2009 Wiley Periodicals, Inc. J Comput Client 30: 864-872, 2009

引用

页码：864 / 872

页数：9

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