GROMACS is an incredibly powerful open-source software package used to run classical molecular dynamics simulations. It is well documented, comes with an amazing suite of in-build analysis tools, and is lightning fast. Yet, it is devilishly difficult to learn (at least, in my experience).

My major grievance with GROMACS is the formatting of its topologies. GROMACS tends to hide a lot of topological information obfuscated within external files, often within seemingly hidden library files.

The key to understanding what is actually going on is to include the -pp flag within the pre-processing command grompp. Such as:

gmx grompp -f md_parameters.mdp -c input_structure.gro -p topology.top -pp

In so doing, not only will you produce your usual topol.tpr runfile, but also a new file, processed.top.

This new topology file contains all of the information needed to run your MD simulation, including all the information kept within your initial topology.top file, along with all the topological parameters that may be nested within hidden files and libraries.

Going forward, I then use this processed.top file for all my simulations. It’s bigger than the initial topology file, but I can clearly see how to structure a GROMACS topology, deal with error codes with ease, and can make quick edits to a forcefield if needed.