GROMACS¶

GROMACS is a software suite for high-performance molecular dynamics and output analysis. The bundle packages version 2024.5. Four variants are available:

SSE4.1 without CUDA
AVX2_256 without CUDA
AVX2_256 with CUDA compute capability 70
AVX_512 with CUDA compute capability 70
AVX2_256 with CUDA compute capability 86
AVX_512 with CUDA compute capability 86

Usage example¶

The following command can be executed in the terminal to load the bundle:

1	`module load gromacs`

The default variant depends on the availability of SIMD instructions and CUDA GPUs. A specific variant can be loaded, for example:

module load gromacs simd=AVX2_256 cuda=70

The module makes the gmx and gmx_mpi commands available. The gromacs_shell command can be used to access a shell in the bundle.

No snippets are provided consult tutorials for usage examples.

Performance notes¶

No performance notes available

Recommended resources¶

GROMACS should be run on a system with at least 16 GB of RAM, 16 threads, and equipped with a CUDA GPU. Recommended resources taken from:

Benchmarks¶

No benchmarks available.

Community guides and tutorials¶

No community guides available.

Official site and documentation¶

Licensing information¶

GROMACS is available under the GNU LGPL v2.1.

Primary citation¶

GROMACS 2024.5 Source code Mark Abraham, Andrey Alekseenko, Vladimir Basov, Cathrine Bergh, Eliane Briand, Ania Brown, Mahesh Doijade, Giacomo Fiorin, Stefan Fleischmann, Sergey Gorelov, Gilles Gouaillardet, Alan Gray, M. Eric Irrgang, Farzaneh Jalalypour, Joe Jordan, Carsten Kutzner, Justin A. Lemkul, Magnus Lundborg, Pascal Merz, Vedran Miletic, Dmitry Morozov, Julien Nabet, Szilard Pall, Andrea Pasquadibisceglie, Michele Pellegrino, Hubert Santuz, Roland Schulz, Tatiana Shugaeva, Alexey Shvetsov, Alessandra Villa, Sebastian Wingbermuehle, Berk Hess, Erik Lindahl doi

External guides and resources¶

If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za