GROMACS
| 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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[edit] History
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.
[edit] Features
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:
- computation of the virial in a single, rather than in a double sum over particles;
- generic representation of all possible periodic box types as triclinic;
- optimized handling of the neighbor list by storage of translation vectors to the nearest neighbor in a periodic system;
- a specialized routine for the calculation of the inverse square root;
- the use of cubic spline interpolation from tabulated values for the evaluation of force/energy;
- a fast grid-based neighbor searching; and
- the use of multimedia (3DNow! and SSE) instructions on Pentium (III and higher), Athlon, and Duron processors.
The highly optimized code makes GROMACS one of the fastest programs for molecular simulations to date[citation needed]. In addition, support for different force fields makes GROMACS very flexible. For example, AMBER, CHARMM can be applied to GROMACS.
[edit] Uses
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]
[edit] See also
- OPLS
- GROMOS
- CHARMM
- NAMD
- Yasara
- Force field implementation
- Abalone
- Grace (plotting tool)
- Folding@home
- List of software for molecular mechanics modeling
- Molecular design software
- VOTCA
- Bennett acceptance ratio
- VisIt
[edit] References
- ^ Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ (2005). "GROMACS: fast, flexible, and free". J Comput Chem 26 (16): 1701–18. doi:10.1002/jcc.20291. PMID 16211538.
- ^ Hess B, Kutzner C, Van Der Spoel D, Lindahl E (2008). "GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation". J Chem Theory Comput 4 (2): 435. doi:10.1021/ct700301q.
- ^ GROMACS flow chart, GROMACS Manual
- ^ FAQ-Open Source, Folding@Home
- ^ Markoff, John (2009-09-29). "Wanted: Home Computers to Join in Research on Artificial Life". The New York Times. http://www.nytimes.com/2009/09/29/science/29grid.html?ref=science.
