GROMACS: Fast, flexible, and free

Van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E. and Berendsen, H. J. C. (2005) GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26 16: 1701-1718. doi:10.1002/jcc.20291


Author Van der Spoel, D.
Lindahl, E.
Hess, B.
Groenhof, G.
Mark, A. E.
Berendsen, H. J. C.
Title GROMACS: Fast, flexible, and free
Journal name Journal of Computational Chemistry   Check publisher's open access policy
ISSN 0192-8651
Publication date 2005-01-01
Sub-type Critical review of research, literature review, critical commentary
DOI 10.1002/jcc.20291
Volume 26
Issue 16
Start page 1701
End page 1718
Total pages 18
Place of publication Hoboken
Publisher John Wiley & Sons Inc
Language eng
Abstract This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily Customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromaes.org. (c) 2005 Wiley Periodicals. Inc.
Keyword Chemistry, Multidisciplinary
GROMACS
molecular simulation software
molecular dynamics
free energy computation
parallel computation
Molecular-dynamics Simulations
Photoactive Yellow Protein
Free-energy Differences
X-ray Crystallography
Particle Mesh Ewald
Liquid Water
Force-field
Boundary-conditions
Ompf Porin
Numerical-integration
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown
Additional Notes This document is a journal review.

Document type: Journal Article
Sub-type: Critical review of research, literature review, critical commentary
Collections: Excellence in Research Australia (ERA) - Collection
School of Chemistry and Molecular Biosciences
 
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Created: Thu, 20 Sep 2007, 03:58:48 EST