OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

被引：546

作者：

Eastman, Peter ^{[1
]}

Friedrichs, Mark S. ^{[1
]}

Chodera, John D. ^{[2
]}

Radmer, Randall J. ^{[3
]}

Bruns, Christopher M. ^{[4
]}

Ku, Joy P. ^{[1
]}

Beauchamp, Kyle A. ^{[5
]}

Lane, Thomas J. ^{[6
]}

Wang, Lee-Ping ^{[6
]}

Shukla, Diwakar ^{[6
]}

Tye, Tony ^{[7
]}

Houston, Mike ^{[7
]}

Stich, Timo ^{[8
]}

Klein, Christoph ^{[9
]}

Shirts, Michael R. ^{[9
]}

Pande, Vijay S. ^{[6
,10
]}

机构：

[1] Stanford Univ, Dept Bioengn, Stanford, CA 94035 USA

[2] Univ Calif Berkeley, Calif Inst Quantitat Biosci QB3, Berkeley, CA 94720 USA

[3] SLAC Natl Accelerator Lab, Menlo Pk, CA 94025 USA

[4] Howard Hughes Med Inst, Ashburn, VA 20147 USA

[5] Stanford Univ, Biophys Program, Stanford, CA 94035 USA

[6] Stanford Univ, Dept Chem, Stanford, CA 94035 USA

[7] Adv Micro Devices Inc, Sunnyvale, CA 94088 USA

[8] NVIDIA GmbH, Wurselen, Germany

[9] Univ Virginia, Dept Chem Engn, Charlottesville, VA 22904 USA

[10] Stanford Univ, Dept Comp Sci, Stanford, CA 94035 USA

来源：

JOURNAL OF CHEMICAL THEORY AND COMPUTATION | 2013年 / 9卷 / 01期

关键词：

FREE-ENERGY CALCULATIONS; DYNAMICS SIMULATIONS; FORCE-FIELDS; MECHANICS; EFFICIENT; MODEL; DISPERSION; WATER;

D O I：

10.1021/ct300857j

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

OpenMM is a software toolkit for performing molecular simulations on a range of high performance computing architectures. It is based on a layered architecture: the lower layers function as a reusable library that can be invoked by any application, while the upper layers form a complete environment for running molecular simulations. The library API hides all hardware-specific dependencies and optimizations from the users and developers of simulation programs: they can be run without modification on any hardware on which the API has been implemented. The current implementations of OpenMM include support for graphics processing units using the OpenCL and CUDA frameworks. In addition, OpenMM was designed to be extensible, so new hardware architectures can be accommodated and new functionality (e.g., energy terms and integrators) can be easily added.

引用

页码：461 / 469

页数：9

共 48 条

[1]

Aaftab M., 2008, OPENCL SPECIFICATION

[2] MOLECULAR MECHANICS - THE MM3 FORCE-FIELD FOR HYDROCARBONS .1. [J].