...

• 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.

...

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..

Python

Python packages, MDAnalysis and MDTraj, can read and write trajectory- and coordinate-files of GROMACSand both have a variety of used analysis functions. Both packages integrate well with Python's data-science packages like NumPy, SciPy and Pandas, and with plotting libraries such as Matplotlib.

Usage tips

System preparation

Your tpr file (portable binary run input file) contains your initial structure, molecular topology and all of the simulation parameters. Tpr files are portable can be copied from one computer to another one, but you should always use the same version of mdrun and grompp. Mdrun is able to use tpr files that have been created with an older version of grompp, but this can cause unexpected results in your simulation.

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.

...

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