title: GROMACS: fast, flexible, and free.
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.gromacs.org.
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, S-75124 Uppsala, Sweden.
authors.forename: David
authors.initials: D
authors.lastname: Van Der Spoel
authors.forename: Erik
authors.initials: E
authors.lastname: Lindahl
authors.forename: Berk
authors.initials: B
authors.lastname: Hess
authors.forename: Gerrit
authors.initials: G
authors.lastname: Groenhof
authors.forename: Alan E
authors.initials: AE
authors.lastname: Mark
authors.forename: Herman J C
authors.initials: HJ
authors.lastname: Berendsen
mesh_terms: D000465:Algorithms; D002462:Cell Membrane / Q000737:chemistry; D003198:Computer Simulation / Q000639:trends*; D008565:Membrane Proteins / Q000737:chemistry; D008956:Models, Chemical; D015394:Molecular Structure; D017510:Protein Folding; D012984:Software; D013269:Stochastic Processes; D013816:Thermodynamics
chemical_list: D008565:Membrane Proteins