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35 \documentclass[11pt,
a4paper,twoside
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}
36 \usepackage{here,picins,fancy,array,tabularx,multicol,dcolumn,makeidx,times,ifthen,enumitem,longtable,pdflscape
}
37 %citesort was old, deprecated in tex, and doesn't work with hyperref/pdftex.
38 %it is rumored you could achieve the same functionality with natbib, but
39 %after a couple of hours of trial I gave up... /EL
42 \usepackage[utf8
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43 \usepackage[T1]{fontenc}
45 \newcommand{\projectContributors}{
46 Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, \\
47 Aldert van Buuren, P\"ar Bjelkmar, Rudi van Drunen, \\
48 Anton Feenstra, Sebastian Fritsch, Gerrit Groenhof, \\
49 Christoph Junghans, Jochen Hub, Peter Kasson, \\
50 Carsten Kutzner, Brad Lambeth, Per Larsson, \\
51 Justin A. Lemkul, Magnus Lundborg, Erik Marklund, Peiter Meulenhoff, \\
52 Teemu Murtola, Szil\'ard P\'all, Sander Pronk, \\
53 Roland Schulz, Michael Shirts, Alfons Sijbers, \\
54 Peter Tieleman, Christian Wennberg and Maarten Wolf.
56 \newcommand{\projectLeaders}{
57 Mark Abraham, Berk Hess, David van der Spoel, and Erik Lindahl.
63 Author=
{The GROMACS team.
64 Contributors:
\projectContributors
65 Project leaders:
\projectLeaders
66 For more details see http://www.gromacs.org/About
\_Gromacs/People
},
67 Title=
{GROMACS Reference Manual
},
68 Subject=
{Theoretical and algorithmic background to molecular dynamics simulation using GROMACS
},
69 Keywords=
{GROMACS; molecular dynamics; molecular simulation; free energy; SIMD; GPU; GPGPU; MPI; OpenMP
}
74 %roman pagenumbers for the preamble stuff
77 % Adjust margins on front page to make it
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103 %{\fontsize{30}{36} \selectfont \bf Version \gmxver}
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115 \renewcommand{\chaptermark}[1]{\markboth{#1}{#1}} % remember chapter title
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117 % section number and title
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125 {\fontsize{40}{50} \selectfont
127 Reference Manual\\
[1cm
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129 {\LARGE\bf Version
\gmxver}\\
[1cm
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132 Contributions from \\
135 \projectContributors}
138 {\LARGE \projectLeaders}
145 \noindent \copyright\
1991--
2000:
146 Department of Biophysical Chemistry, University of Groningen. \\
147 Nijenborgh
4,
9747 AG Groningen, The Netherlands.\\
150 \noindent \copyright\
2001--
{\gmxyear}:
151 The
{\gromacs} development teams at the Royal Institute of Technology and \\
152 Uppsala University, Sweden.
156 More information can be found on our website:
{\wwwpage}.
160 \pagestyle{fancyplain
}
162 \subsection*
{Preface \& Disclaimer
}
163 This manual is not complete and has no pretention to be so due
164 to lack of time of the contributors -- our first priority is to improve
165 the software. It is worked on continuously,
166 which in some cases might mean the information is not entirely correct.
168 Comments on form and content are welcome, please send them to one of
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170 at
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171 source repository and uploaded to
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173 We release an updated version of the manual whenever
174 we release a new version of the software, so in general
175 it is a good idea to use a manual with the same major and
176 minor release number as your
{\gromacs} installation.
178 \subsection*
{On-line Resources
}
179 You can find more documentation and other material at our homepage
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181 {\gromacs} mailing lists with archives and contributed
182 topologies/force fields.
184 \subsection*
{Citation information
}
185 When
\normindex{citing
} this
document in any scientific publication
186 please refer to it as:
189 M.J. Abraham, D. van der Spoel, E. Lindahl, B. Hess, and the GROMACS development team,
190 \hspace{0.3em
} {\em {\gromacs} {U
}ser
{M
}anual version
\gmxver},
191 \hspace{0.3em
} {\wwwpage} (
{\gmxyear})
193 However, we prefer that you cite (some of) the
{\gromacs}
194 papers~
\cite{Bekker93a,Berendsen95a,Lindahl2001a,Spoel2005a,Hess2008b,Pronk2013,Pall2015,Abraham2015
}
195 when you publish your results. Any future development depends on academic research
196 grants, since the package is distributed as free software!
198 \subsection*
{{\gromacs} is
{\em Free Software
}}
199 The entire
{\gromacs} package is available under the GNU Lesser
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2.1. This means it's free as in free
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206 \href{http://www.gnu.org/licenses/old-licenses/lgpl-
2.1.html
}{http://www.gnu.org/licenses/old-licenses/lgpl-
2.1.html
}.
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{\gromacs} source code and and selected set of binary packages are
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\wwwpage. Have fun.
219 % R E A L M A N U A L
222 \pagenumbering{arabic
}
234 % A P P E N D I C E S
241 % The pdfdummy counter is a workaround to get correct
242 % bookmarks for the index & bibliography in pdf files
244 \newcounter{pdfdummy
}
247 % B I B L I O G R A P H Y
250 \refstepcounter{pdfdummy
}
252 \addcontentsline{toc
}{chapter
}{Bibliography
}
254 \bibliographystyle{proteins
}
255 \bibliography{monster,unpubl
}
261 \refstepcounter{pdfdummy
}
263 \addcontentsline{toc
}{chapter
}{Index
}
265 \renewcommand{\see}[2]{\mbox{} \mbox{\textit{see
} #1}}
270 % LocalWords: Groningen der Spoel Lindahl Nijenborgh Carsten Kutzner Aldert
271 % LocalWords: Buuren Apol Meulenhoff Tieleman Sijbers Feenstra Rudi Drunen Sij
272 % LocalWords: Berendsen pretention bers ser anual Uppsala Mainz unpubl
273 % LocalWords: Bioinformatics GROMACS Rossen Apostolov ar Bjelkmar
274 % LocalWords: Fritsch Gerrit Groenhof Junghans Kasson Larsson Peiter
275 % LocalWords: Teemu Murtola Szil ard Pronk Jochen Lambeth Lemkul
276 % LocalWords: Marklund Maarten