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

被引：16768

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

共 48 条

[1]

Pronk S., Pall S., Schulz R., Larsson P., Bjelkmar P., Apostolov R., Et al., Bioinf, 29, pp. 845-854, (2013)

[2]

Case D.A., Cheatham T.E., Darden T., Gohlke H., Luo R., Merz K.M., Et al., J Comput Chem, 26, pp. 1668-1688, (2005)

[3]

Phillips J.C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Et al., J Comput Chem, 26, pp. 1781-1802, (2005)

[4]

Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M., J Comput Chem, 4, pp. 187-217, (1983)

[5]

Plimpton S., J Comp Phys, 117, pp. 1-19, (1995)

[6]

Bowers K.J., Chow E., Xu H., Dror R.O., Eastwood M.P., Gregersen B.A., Proceedings of the ACM/IEEE conference on supercomputing

[7]

, (2006)

[8]

Shirts M., Pande V.S., Science, 290, pp. 1903-1904, (2000)

[9]

Tribello G.A., Bonomi M., Branduardi D., Camilloni C., Bussi G., Comput Phys Commun, 185, pp. 604-613, (2014)

[10]

Marrink S.J., Risselada H.J., Yefimov S., Tieleman D.P., de Vries A.H., J Phys Chem B, 111, pp. 7812-7824, (2007)

← 1 2 3 4 5 →