Getting started

In this chapter we assume the reader is familiar with Molecular Dynamics and familiar with Unix, including the use of a text editor such as jot, emacs or vi. We furthermore assume the GROMACS software is installed properly on your system. When you see a line like

ls -l

you are supposed to type the contents of that line on your computer terminal.

Setting up your environment

In order to check whether you have access to GROMACS, please start by entering the command:

gmx -version

This command should print out information about the version of GROMACS installed. If this, in contrast, returns the phrase

gmx: command not found.

then you have to find where your version of GROMACS is installed. In the default case, the binaries are located in /usr/local/gromacs/bin, however, you can ask your local system administrator for more information, and then follow the advice for Getting access to GROMACS after installation.

Flowchart of typical simulation

A typical simulation workflow with GROMACS is illustrated here.

Important files

Here is an overview of the most important GROMACS file types that you will encounter.

Molecular Topology file (.top)

The molecular topology file is generated by the program gmx pdb2gmx. gmx pdb2gmx translates a pdb structure file of any peptide or protein to a molecular topology file. This topology file contains a complete description of all the interactions in your peptide or protein.

Molecular Structure file (.gro, .pdb)

When gmx pdb2gmx is executed to generate a molecular topology, it also translates the structure file (pdb file) to a GROMOS structure file (gro file). The main difference between a pdb file and a gromos file is their format and that a gro file can also hold velocities. However, if you do not need the velocities, you can also use a pdb file in all programs. To generate a box of solvent molecules around the peptide, the program gmx solvate is used. First the program gmx editconf should be used to define a box of appropriate size around the molecule. gmx solvate solvates a solute molecule (the peptide) into any solvent (in this case, water). The output of gmx solvate is a gromos structure file of the peptide solvated in water. gmx solvate also changes the molecular topology file (generated by gmx pdb2gmx) to add solvent to the topology.

Molecular Dynamics parameter file (.mdp)

The Molecular Dynamics Parameter (mdp) file contains all information about the Molecular Dynamics simulation itself e.g. time-step, number of steps, temperature, pressure etc. The easiest way of handling such a file is by adapting a sample mdp file. A sample mdp file is available.

Index file (.ndx)

Sometimes you may need an index file to specify actions on groups of atoms (e.g. temperature coupling, accelerations, freezing). Usually the default index groups will be sufficient, so for this demo we will not consider the use of index files.

Run input file (.tpr)

The next step is to combine the molecular structure (gro file), topology (top file) MD-parameters (mdp file) and (optionally) the index file (ndx) to generate a run input file (tpr extension). This file contains all information needed to start a simulation with GROMACS. The gmx grompp program processes all input files and generates the run input tpr file.

Trajectory file (.trr, .tng, or .xtc)

Once the run input file is available, we can start the simulation. The program which starts the simulation is called gmx mdrun (or sometimes just mdrun, or mdrun_mpi). The only input file of gmx mdrun that you usually need in order to start a run is the run input file (tpr file). The typical output files of gmx mdrun are the trajectory file (trr file), a logfile (log file), and perhaps a checkpoint file (cpt file).

Tutorial material

There are many tutorials available that cover aspects of using GROMACS.

Background reading

• Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., Hermans, J. (1981) Intermolecular Forces, chapter Interaction models for water in relation to protein hydration, pp 331-342. Dordrecht: D. Reidel Publishing Company Dordrecht
• Kabsch, W., Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577–2637.
• Mierke, D.F., Kessler, H. (1991). Molecular dynamics with dimethyl sulfoxide as a solvent. Conformation of a cyclic hexapeptide. J. Am. Chem. Soc. 113, 9446.
• Stryer, L. (1988). Biochemistry vol. 1, p. 211. New York: Freeman, 3 edition.