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GROMACS: fast, flexible, and free
Uppsala University.
Stockholm University.ORCID-id: 0000-0002-2734-2794
Max-Planck Institut Mainz.ORCID-id: 0000-0002-7498-7763
Max-Planck Institut Göttingen.
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2005 (Engelska)Ingår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 26, nr 16, s. 1701-1718Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

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.

Ort, förlag, år, upplaga, sidor
2005. Vol. 26, nr 16, s. 1701-1718
Nyckelord [en]
GROMACS, molecular simulation software, molecular dynamics, free energy computation, parallel computation
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Biofysik Teoretisk kemi
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URN: urn:nbn:se:kth:diva-82629DOI: 10.1002/jcc.20291ISI: 000233021400004PubMedID: 16211538OAI: oai:DiVA.org:kth-82629DiVA, id: diva2:498429
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QC 20120301Tillgänglig från: 2012-02-12 Skapad: 2012-02-12 Senast uppdaterad: 2017-12-07Bibliografiskt granskad

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