Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit

被引：109

作者：

Eastman, Peter ^{[1
]}

Pande, Vijay S. ^{[2
]}

机构：

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

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

来源：

JOURNAL OF COMPUTATIONAL CHEMISTRY | 2010年 / 31卷 / 06期

关键词：

molecular dynamics; graphics processing unit; GPU; nonbonded; cutoff; reaction field; explicit solvent; water; LAMBDA-REPRESSOR; SIMULATIONS;

D O I：

10.1002/jcc.21413

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

We describe an algorithm for computing nonbonded interactions with cutoffs on a graphics processing unit. We have incorporated it into OpenMM, a library for performing molecular simulations on high-performance computer architectures. We benchmark it on a variety of systems including boxes of water molecules, proteins in explicit solvent, a lipid bilayer, and proteins with implicit solvent. The results demonstrate that its performance scales linearly with the number of atoms over a wide range of system sizes, while being significantly faster than other published algorithms. (C) 2009 Wiley Periodicals. Inc. J Comput Chem 31: 1268-1272, 2010

引用

页码：1268 / 1272

页数：5

共 21 条

[1]

Allen M. P., 1987, COMPUTER SIMULATION

[2] General purpose molecular dynamics simulations fully implemented on graphics processing units [J].