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很全很详细的gromacs介绍,这是对于gromacs初学者的最好工具,全面清晰的介绍
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GROMACS
Groningen Machine for Chemical Simulations
USER MANUAL
Version 4.5.4
GROMACS
USER MANUAL
Version 4.5.4
Written by
Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, P
¨
ar Bjelkmar, Rudi van Drunen,
Anton Feenstra, Gerrit Groenhof, Peter Kasson,
Per Larsson, Peiter Meulenhoff, Teemu Murtola,
Szil
´
ard P
´
all, Sander Pronk, Roland Schulz,
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 gromacs@gromacs.org, 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.
On-line Resources
You can find more documentation and other material at our homepage www.gromacs.org. Among
other things there is an on-line reference, several GROMACS mailing lists with archives and
contributed topologies/force fields.
Citation information
When citing this document in any scientific publication please refer to it as:
D. van der Spoel, E. Lindahl, B. Hess, A. R. van Buuren, E. Apol, P. J. Meulenhoff,
D. P. Tieleman, A. L. T. M. Sijbers, K. A. Feenstra, R. van Drunen and H. J. C.
Berendsen, Gromacs User Manual version 4.5.4, www.gromacs.org (2010)
However, we prefer that you cite (some of) the GROMACS papers [1, 2, 3, 4, 5] when you publish
your results. Any future development depends on academic research grants, since the package is
distributed as free software!
Current development
GROMACS is a joint effort, with contributions from lots of developers around the world. The core
development is currently taking place at
• Department of Cellular and Molecular Biology, Uppsala University, Sweden.
(David van der Spoel).
• Stockholm Bioinformatics Center, Stockholm University, Sweden
(Erik Lindahl).
• Stockholm Bioinformatics Center, Stockholm University, Sweden
(Berk Hess)
v
GROMACS is Free Software
The entire GROMACS package is available under the GNU General Public License. This means
it’s free as in free speech, not just that you can use it without paying us money. For details, check
the COPYING file in the source code or consult www.gnu.org/copyleft/gpl.html.
The GROMACS source code and and selected set of binary packages are available on our home-
page, www.gromacs.org. Have fun.
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- 边边的账号2014-08-08话说已经出到5.0了。
- u0102232722013-10-21内容很全面
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