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Read more on the GROMACS home page.

For a manual consult the the GROMACS home page.

Strengths

• 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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*Release notes can be find here. 

These modules can be loaded by using a module load command. Note that Intel MPI module file should be loaded first:

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VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting,  it is free of charge, and includes source code.

Usage

System preparation

Running simulations

Simulations often take longer time than the maximum walltime. By using mdrun with -maxh command will tell the program the requested walltime and  GROMACS will finishes the simulation when reaching 99% of the walltime. At this time, mdrun creates a new checkpoint file and properly close all output files. Using this method, the simulation can be easily restarted from this checkpoint file.

mpirun gmx_mpi mdrun MDRUNARGUMENTS -maxh 24

Restarting simulations

In order to restart a simulation from checkpoint file you can use the same mdrun command as the original simulation and adding -cpi filename.cpt  where the filename is the name of your most recent checkpoint file.

mpirun gmx_mpi mdrun MDRUNARGUMENTS -cpi filename.cpt

More detailed information can be find here.

Performance 

GROMACS prints information about statistics and performance at the end of the md.log file which usually also contains helpful tips to further improve the performance. The performance of the simulation is usually given in ns/day (number if nanoseconds of MD-trajectories simulated within a day).

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

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