GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
Mark James Abraham,
Teemu Murtola,
Roland Schulz,
Szilárd Páll,
Jeremy C. Smith,
Berk Hess,
Erik Lindahl
Affiliations
Mark James Abraham
Theoretical Biophysics, Science for Life Laboratory, KTH Royal Institute of Technology, 17121 Solna, Sweden; Corresponding author.
Teemu Murtola
Center for Biomembrane Research, Department of Biochemistry & Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
Roland Schulz
Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, United States; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996, United States
Szilárd Páll
Theoretical Biophysics, Science for Life Laboratory, KTH Royal Institute of Technology, 17121 Solna, Sweden
Jeremy C. Smith
Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, United States; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996, United States
Berk Hess
Theoretical Biophysics, Science for Life Laboratory, KTH Royal Institute of Technology, 17121 Solna, Sweden
Erik Lindahl
Theoretical Biophysics, Science for Life Laboratory, KTH Royal Institute of Technology, 17121 Solna, Sweden; Center for Biomembrane Research, Department of Biochemistry & Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
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. Keywords: Molecular dynamics, GPU, SIMD, Free energy
