GROMACS Groningen Machine for Chemical Simulations USER MANUAL Version 4.5 GROMACS USER MANUAL Version 4.5 Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Par¨ Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff, Teemu Murtola, Szilard´ Pall,´ Sander Pronk, Roland Schultz, Michael Shirts, Alfons Sijbers, Peter Tieleman Berk Hess, David van der Spoel, and Erik Lindahl. Additional contributions by Mark Abraham, Christoph Junghans, Carsten Kutzner, Justin A. Lemkul, Erik Marklund, Maarten Wolf. c 1991–2000: Department of Biophysical Chemistry, University of Groningen. Nijenborgh 4, 9747 AG Groningen, The Netherlands. c 2001–2010: The GROMACS development teams at the Royal Institute of Technology and Uppsala University, Sweden. More information can be found on our website: www.gromacs.org. iv Preface & Disclaimer This manual is not complete and has no pretention to be so due to lack of time of the contributors – our first priority is to improve the software. It is worked on continuously, which in some cases might mean the information is not entirely correct. Comments are welcome, please send them by e-mail to
[email protected], or to one of the mailing lists (see www.gromacs.org). We try to release an updated version of the manual whenever we release a new version of the soft- ware, so in general it is a good idea to use a manual with the same major and minor release number as your GROMACS installation. Any revision numbers (like 3.1.1) are however independent, to make it possible to implement bug fixes and manual improvements if necessary.