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

Mark James Abraham, Teemu Murtola, Roland Schulz, Szilard Pall, Jeremy C. Smith, Berk Hess, Erik Lindahl
Theoretical Biophysics, Science for Life Laboratory, KTH Royal Institute of Technology, 17121 Solna, Sweden
SoftwareX, 2015

   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 P{‘a}ll, Szil{‘a}rd and Smith, Jeremy C and Hess, Berk and Lindahl, Erik},





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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.
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