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

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:
Grant/Contract Number:
AC05-00OR22725
Type:
Published Article
Journal Name:
SoftwareX
Additional Journal Information:
Journal Volume: 1-2; Journal Issue: C; Journal ID: ISSN 2352-7110
Publisher:
Elsevier
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)
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; Molecular dynamics; GPU; SIMD; Free energy
OSTI Identifier:
1252791
Alternate Identifier(s):
OSTI ID: 1376606