Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

被引：15579

作者：

Abraham, Mark James ^{[1
]}

Murtola, Teemu ^{[4
]}

Schulz, Roland ^{[2
,3
]}

Páll, Szilárd ^{[1
]}

Smith, Jeremy C. ^{[2
,3
]}

Hess, Berk ^{[1
]}

Lindah, Erik ^{[1
,4
]}

机构：

[1] Theoretical Biophysics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna

[2] Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, 37831, TN

[3] Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, 37996, TN

[4] Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm

来源：

SoftwareX | 2015年 / 1-2卷

基金：

欧洲研究理事会;

关键词：

Free energy; Gpu; Molecular dynamics; Simd;

D O I：

10.1016/j.softx.2015.06.001

中图分类号：

学科分类号：

摘要：

GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. These work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU-GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. The latest best-in-class compressed trajectory storage format is supported. © 2015 The Authors.

引用

页码：19 / 25

页数：6

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