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

Abstract

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. This 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. Finally, the latest best-in-class compressed trajectory storage format is supported.

Authors:
ORCiD logo [1];  [2];  [3];  [1];  [3];  [1];  [4]
  1. KTH Royal Inst. of Technology, Stockholm (Sweden)
  2. Stockholm Univ. (Sweden). Center for Biomembrane Research
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States). Dept. of Biochemistry and Cellular and Molecular Biology
  4. KTH Royal Inst. of Technology, Stockholm (Sweden); Stockholm Univ. (Sweden). Center for Biomembrane Research
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1252791
Alternate Identifier(s):
OSTI ID: 1376606
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Published Article
Journal Name:
SoftwareX
Additional Journal Information:
Journal Volume: 1-2; Journal Issue: C; Journal ID: ISSN 2352-7110
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; Molecular dynamics; GPU; SIMD; Free energy

Citation Formats

Abraham, Mark James, Murtola, Teemu, Schulz, Roland, Páll, Szilárd, Smith, Jeremy C., Hess, Berk, and Lindahl, Erik. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. United States: N. p., 2015. Web. doi:10.1016/j.softx.2015.06.001.
Abraham, Mark James, Murtola, Teemu, Schulz, Roland, Páll, Szilárd, Smith, Jeremy C., Hess, Berk, & Lindahl, Erik. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. United States. doi:10.1016/j.softx.2015.06.001.
Abraham, Mark James, Murtola, Teemu, Schulz, Roland, Páll, Szilárd, Smith, Jeremy C., Hess, Berk, and Lindahl, Erik. Wed . "GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers". United States. doi:10.1016/j.softx.2015.06.001.
@article{osti_1252791,
title = {GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers},
author = {Abraham, Mark James and Murtola, Teemu and Schulz, Roland and Páll, Szilárd and Smith, Jeremy C. and Hess, Berk and Lindahl, Erik},
abstractNote = {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. This 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. Finally, the latest best-in-class compressed trajectory storage format is supported.},
doi = {10.1016/j.softx.2015.06.001},
journal = {SoftwareX},
number = C,
volume = 1-2,
place = {United States},
year = {2015},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1016/j.softx.2015.06.001

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