Description

GROMACS is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers and fluid dynamics.

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• GROMACS provides extremely high performance compared to all other programs.
• GROMACS can make simultaneous use of both CPU and GPU available in a system. There are options to statically and dynamically balance the load between the different resources.
• GROMACS is user-friendly, with topologies and parameter files written in clear text format.
• Both run input files and trajectories are independent of hardware endian-ness, and can thus be read by any version GROMACS.
• GROMACS comes with a large selection of flexible tools for trajectory analysis.
• GROMACS can be run in parallel, using the standard MPI communication protocol.
• GROMACS contains several state-of-the-art algorithms.
• GROMACS is Free Software, available under the GNU Lesser General Public License (LGPL).

Weaknesses

• GROMACS does not do to much further analysis to get very high simulation speed.
• Sometimes it is challenging to get non-standard information about the simulated system.
• Different versions sometimes have differences in default parameters/methods. Reproducing older version simulations with a newer version can be difficult.
• Additional tools and utilities provided by GROMACS are sometimes not the top quality.

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Note: Settings of the Thread-MPI ranks and OpenMP threads is for achieve optimal performance. The number of ranks should be a multiple of the number of sockets, and the number of cores per node should be a multiple of the number of threads per rank.

Related Modules

Gromacs-Plumed

PLUMED is an open-source, community-developed library that provides a wide range of different methods, such as enhanced-sampling algorithms, free-energy methods and tools to analyze the vast amounts of data produced by molecular dynamics (MD) simulations. PLUMED works together with some of the most popular MD engines.

Gromacs/20XX.X-plumed modules are versions have been patched with PLUMED's modifications, and these versions are able to run meta-dynamics simulations.

Analyzing results

GROMACS Tools

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More information about performance of the simulations and "how to imporve perfomance" can be find here. 

Special Performance Instructions for Emmy at GWDG

Turbo-boost has been mostly disabled on Emmy at GWDG (partitions medium40, large40, standard96, large96, and huge96) in order to save energy. However, this has a particularly strong performance impact on GROMACS in the range of 20-40%. Therefore, we recommend that GROMACS jobs be submitted requesting turbo-boost to be enabled with the --constraint=turbo_on option given to srun or sbatch.

Useful links

• GROMACS Manuals and documentation
• GROMACS Community Forums
• Useful MD Tutorials for GROMACS
• VMD Visual Molecular Dynamics

References

1. GROMACS User-Guide
2. PLUMED Home