Gromacs: Molecular Dynamics
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About Gromacs
Like NAMD, Gromacs is a molecular dynamics program. GROMACS stands for GROningen MAchine for Chemical Simulation, originally developed at the The University of Groningen in the Netherlands. In addition, the Gromacs gmxbench suite is commonly used for benchmarking.
If you're looking for a how-to on Gromacs installation, skip ahead to the next section. Otherwise, read on for a basic description of the three different file types that Gromacs takes as input.
Gromacs Files
Each example file in the gmxbench suite contains three files - a .gro, .mpd, and .top. Each of these files is used by the Gromacs preprocessor (grompp), a binary that prepares the code to be run in parallel. These are what set up the simulation to be run.
.gro Files
conf.gro and .gro files in general specify the initial positions and velocities of the atoms. Output files with the results from Gromacs runs will also have this format, called Gromos87 format. Each line gives the information for one atom. A typical line might look like this:
9ALA N 87 3.492 2.996 1.618 0.1574 0.2410 -0.0154
- 9ALA is the name of the residue (group of atoms) that this atom belongs to
- N is the kind of atom (nitrogen in this case)
- 87 is the unique id assigned to this atom
- 3.492, 2.996, 1.618 are the x, y, and z positions of the atom
- 0.1574, 0.2410, -0.0154 are the x, y, and z velocities of the atom
For more information, see the gro page on the GROMACS online reference manual.
.mdp Files
.mpd files, including the file grompp.mdp included in each example gromacs setup, is a list of parameters to pass to grompp. These include directives about and for the preprocessor. It also includes some of the basic parameters about how to run the molecular dynamics simulations, including what types of processing to use and what form the output should take.
For more information, see the mdp options page on the GROMACS online reference manual.
.top Files
.top files, including the topol.top files included in the example, are files that grompp uses to construct the topology of a simulation, including the atoms, bonds, and angles.
For more information, see the top example page on the GROMACS online reference manual.
Installing Gromacs
Installing Gromacs is relatively painless and easy to do. Continue on to Gromacs: Installation.
References
- GROMACS: Fast, Free and Flexible MD
- H.J.C. Berendsen, D. van der Spoel and R. van Drunen: GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 pp. 43-56 (1995). Available online at http://www.gromacs.org/documentation/articles/berendsen95a.pdf
