About this Chemistry article

GROMACS: Fast, flexible, and free by David Van Der Spoel; Erik Lindahl; Berk Hess; Gerrit Groenhof; Alan E. Mark; Herman J. C. Berendsen is a Chemistry article available to read on EtoBox.

## 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

Author

David Van Der Spoel; Erik Lindahl; Berk Hess; Gerrit Groenhof; Alan E. Mark; Herman J. C. Berendsen

Publisher

Wiley

Published

2005

Language

EN

Field

Chemistry (Physical Sciences)