| Stable release | 4.5.5 / 20 September 2011 |
|---|---|
| Written in | C, C++, Assembly |
| Operating system | Solaris, Linux, MacOS X, Windows by Cygwin, any other Unix variety |
| Type | Simulation |
| License | GNU General Public License |
| Website | www.gromacs.org |
GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics simulation package originally developed in the University of Groningen, now maintained and extended at different places, including the University of Uppsala, University of Stockholm and the Max Planck Institute for Polymer Research.[1][2] GROMACS is open source software released under the GPL.
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The GROMACS project was originally started to construct a dedicated parallel computer system for molecular simulations, based on a ring architecture. The molecular dynamics specific routines were rewritten in the C programming language from the Fortran77-based program GROMOS, which had been developed in the same group.
The program is written for Unix-like operating systems; it can run on Windows machines if the Cygwin Unix layer is used. The program can be run in parallel on multiple CPU cores or a network of machines using the MPI library.
GROMACS contains a script to convert molecular coordinates from a PDB file into the formats it uses internally. Once a configuration file for the simulation of several molecules (possibly including solvent) has been created, the actual simulation run (which can be time consuming) produces a trajectory file, describing the movements of the atoms over time. This trajectory file can then be analyzed or visualized with a number of supplied tools.[3]
Many specific elements were added during the transition from GROMOS to GROMACS, most notably:
The highly optimized code makes GROMACS one of the fastest programs for molecular simulations to date. In addition, support for different force fields makes GROMACS very flexible. For example, AMBER, CHARMM can be applied to GROMACS.
A notable use of GROMACS is in the distributed computing project Folding@Home, where it is used extensively in the simulation of protein folding. (This version has been granted a non-GPL license.)[4]
EvoGrid, a distributed computing project to evolve artificial life, also employs GROMACS.[5]