manual/gromacs.tex

   1 %
   2 % This file is part of the GROMACS molecular simulation package.
   3 %
   4 % Copyright (c) 2013, by the GROMACS development team, led by
   5 % Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6 % and including many others, as listed in the AUTHORS file in the
   7 % top-level source directory and at http://www.gromacs.org.
   8 %
   9 % GROMACS is free software; you can redistribute it and/or
  10 % modify it under the terms of the GNU Lesser General Public License
  11 % as published by the Free Software Foundation; either version 2.1
  12 % of the License, or (at your option) any later version.
  13 %
  14 % GROMACS is distributed in the hope that it will be useful,
  15 % but WITHOUT ANY WARRANTY; without even the implied warranty of
  16 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17 % Lesser General Public License for more details.
  18 %
  19 % You should have received a copy of the GNU Lesser General Public
  20 % License along with GROMACS; if not, see
  21 % http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22 % Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23 %
  24 % If you want to redistribute modifications to GROMACS, please
  25 % consider that scientific software is very special. Version
  26 % control is crucial - bugs must be traceable. We will be happy to
  27 % consider code for inclusion in the official distribution, but
  28 % derived work must not be called official GROMACS. Details are found
  29 % in the README & COPYING files - if they are missing, get the
  30 % official version at http://www.gromacs.org.
  31 %
  32 % To help us fund GROMACS development, we humbly ask that you cite
  33 % the research papers on the package. Check out http://www.gromacs.org.
  34
  35 \documentclass[11pt,a4paper,twoside]{gmxmanual}
  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
  40 \input{macros}
  41
  42 % If you set gmxlite to 1 a very much shortened version of the manual
  43 % will be generated, which may be useful for teaching.
  44 \newcommand{\gmxlite}{0}
  45
  46 \begin{document}
  47
  48 %roman pagenumbers for the preamble stuff
  49 \pagenumbering{roman}
  50
  51 % Adjust margins on front page to make it
  52 % symmetrical. It is reset on the next page.
  53 \addtolength{\oddsidemargin}{-5mm}
  54
  55 %
  56 %       F R O N T P A G E
  57 %
  58 \pagestyle{empty}
  59 \begin{center}
  60
  61 \textcolor{blue}{\fontsize{84}{96} \selectfont GROMACS}
  62 \vspace{4mm}
  63
  64 \textcolor{blue}{\LARGE \em Groningen Machine for Chemical Simulations}
  65 \vspace{4mm}
  66
  67 \includegraphics[height=5in]{plots/peregrine}
  68 \vspace{4mm}
  69
  70 \ifthenelse{\equal{\gmxlite}{1}}
  71 {
  72 \fcolorbox{blue}{blue}{\textcolor{white}{\fontsize{56}{64} \selectfont User Manual {\em ~Lite~}}}
  73 }
  74 {
  75 \fcolorbox{blue}{blue}{\textcolor{white}{\fontsize{56}{64} \selectfont ~USER MANUAL~}}
  76 } % Brace matches ifthenelse test for gmxlite
  77 \vspace{4mm}
  78
  79 \textcolor{blue}{\fontsize{48}{56} \selectfont ~Version \gmxver~}
  80
  81
  82 %\vspace{0.25cm}
  83 %{\fontsize{30}{36} \selectfont \bf Version \gmxver}
  84
  85 \end{center}
  86 \vfill
  87
  88 \ifthenelse{\equal{\gmxlite}{1}}
  89 {
  90 \newpage
  91 {\bf
  92 This text is a shortened version of the full {\gromacs} manual, written
  93 by David van der Spoel, Berk Hess, Erik Lindahl and others. Please
  94 find further information on our website {\wwwpage}.}
  95
  96 \vspace{2cm}
  97
  98 \noindent \copyright\ 1991--2000:
  99 Department of Biophysical Chemistry, University of Groningen.
 100 Nijenborgh 4, 9747 AG Groningen, The Netherlands.\\
 101 \medskip
 102
 103 \noindent \copyright\ 2001--{\gmxyear}:
 104 The {\gromacs} development teams at the Royal Institute of Technology and \\
 105 Uppsala University, Sweden.
 106 }
 107 {
 108 \cleardoublepage
 109 } % Brace matches ifthenelse test for gmxlite
 110 %reset to normal margins
 111 \addtolength{\oddsidemargin}{5mm}
 112
 113 %
 114 %       P R E F A C E
 115 %
 116 \renewcommand{\chaptermark}[1]{\markboth{#1}{#1}} % remember chapter title
 117 \renewcommand{\sectionmark}[1]{\markright{\thesection\ #1}}
 118                                                 % section number and title
 119 \lhead[\fancyplain{}{\em\thepage}]{\fancyplain{}{\em\rightmark}}
 120 \rhead[\fancyplain{}{\em\leftmark}]{\fancyplain{}{\em\thepage}}
 121 \cfoot{}
 122
 123 \ifthenelse{\equal{\gmxlite}{1}}{}{
 124 \begin{center}
 125 \phantom{ }
 126 \vspace{1cm}
 127 {\fontsize{40}{50} \selectfont
 128 GROMACS\\
 129 USER MANUAL\\[1cm]
 130 }
 131 {\LARGE\bf Version \gmxver}\\[1cm]
 132
 133 {\Large
 134 Contributions from \\
 135 \vspace{5mm}
 136
 137 Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, \\
 138 Aldert van Buuren, P\"ar Bjelkmar, Rudi van Drunen, \\
 139 Anton Feenstra, Sebastian Fritsch, Gerrit Groenhof, \\
 140 Christoph Junghans, Jochen Hub, Peter Kasson, \\
 141 Carsten Kutzner, Brad Lambeth, Per Larsson, \\
 142 Justin A. Lemkul, Erik Marklund, Peiter Meulenhoff, \\
 143 Teemu Murtola, Szil\'ard P\'all, Sander Pronk, \\
 144 Roland Schulz, Michael Shirts, Alfons Sijbers, \\
 145 Peter Tieleman, Christian Wennberg and Maarten Wolf. \\}
 146 \vspace{5mm}
 147
 148 {\LARGE Mark Abraham, Berk Hess, David van der Spoel, and Erik Lindahl.}
 149 \vspace{10mm}
 150 \end{center}
 151
 152 \vfill
 153
 154
 155 \noindent \copyright\ 1991--2000:
 156 Department of Biophysical Chemistry, University of Groningen. \\
 157 Nijenborgh 4, 9747 AG Groningen, The Netherlands.\\
 158 \medskip
 159
 160 \noindent \copyright\ 2001--{\gmxyear}:
 161 The {\gromacs} development teams at the Royal Institute of Technology and \\
 162 Uppsala University, Sweden.
 163
 164 \vspace{5mm}
 165
 166 More information can be found on our website: {\wwwpage}.
 167
 168
 169 \newpage
 170 \pagestyle{fancyplain}
 171
 172 \subsection*{Preface \& Disclaimer}
 173 This manual is not complete and has no pretention to be so due
 174 to lack of time of the contributors -- our first priority is to improve
 175 the software. It is worked on continuously,
 176 which in some cases might mean the information is not entirely correct.
 177
 178 Comments on form and content are welcome, please send them to one of
 179 the mailing lists (see {\wwwpage}), or open an issue
 180 at {\redminepage}. Corrections can also be made in the GROMACS git
 181 source repository and uploaded to {\gerritpage}.
 182
 183 We release an updated version of the manual whenever
 184 we release a new version of the software, so in general
 185 it is a good idea to use a manual with the same major and
 186 minor release number as your {\gromacs} installation.
 187
 188 \subsection*{On-line Resources}
 189 You can find more documentation and other material at our homepage
 190 \wwwpage. Among other things there is an on-line reference, several
 191 {\gromacs} mailing lists with archives and contributed
 192 topologies/force fields.
 193
 194 \subsection*{Citation information}
 195 When \normindex{citing} this document in any scientific publication
 196 please refer to it as:
 197 \begin{quote}
 198 \raggedright
 199 M.J. Abraham, D. van der Spoel, E. Lindahl, B. Hess, and the GROMACS development team,
 200 \hspace{0.3em} {\em {\gromacs} {U}ser {M}anual version \gmxver},
 201 \hspace{0.3em} {\wwwpage} ({\gmxyear})
 202 \end{quote}
 203 However, we prefer that you cite (some of) the {\gromacs}
 204 papers~\cite{Bekker93a,Berendsen95a,Lindahl2001a,Spoel2005a,Hess2008b,Pronk2013}
 205 when you publish your results. Any future development depends on academic research
 206 grants, since the package is distributed as free software!
 207
 208 \subsection*{{\gromacs} is {\em Free Software}}
 209 The entire {\gromacs} package is available under the GNU Lesser
 210 General Public License, version 2.1. This means it's free as in free
 211 speech, not just that you can use it without paying us money. For
 212 details, check the COPYING file in the source code or consult
 213 \href{http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html}{http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html}.
 214
 215 The {\gromacs} source code and and selected set of binary packages are
 216 available on our homepage, \wwwpage. Have fun.
 217 } % Brace matches ifthenelse test for gmxlite
 218
 219 \newpage
 220 %       C O N T E N T S
 221 %
 222 \tableofcontents
 223 %\listoffigures
 224 %\listoftables
 225
 226 %
 227 %       R E A L   M A N U A L
 228 %
 229 \cleardoublepage
 230 \pagenumbering{arabic}
 231
 232 \include{intro}
 233 \include{defunits}
 234 \include{algorithms}
 235 \include{forcefield}
 236
 237 \ifthenelse{\equal{\gmxlite}{1}}{}{
 238 \include{topology}
 239 \include{special}
 240 \include{programs}
 241 } % Brace matches ifthenelse test for gmxlite
 242 \include{analyse}
 243 \ifthenelse{\equal{\gmxlite}{1}}{}{
 244 %
 245 %       A P P E N D I C E S
 246 %
 247 \appendix
 248 \include{install}
 249 \include{implement}
 250 \include{averages}
 251 } % Brace matches ifthenelse test for gmxlite
 252 %
 253 % The pdfdummy counter is a workaround to get correct
 254 % bookmarks for the index & bibliography in pdf files
 255
 256 \newcounter{pdfdummy}
 257
 258 %
 259 %       B I B L I O G R A P H Y
 260 %
 261 \cleardoublepage
 262 \refstepcounter{pdfdummy}
 263
 264 \addcontentsline{toc}{chapter}{Bibliography}
 265
 266 \bibliographystyle{proteins}
 267 \bibliography{monster,unpubl}
 268
 269 %
 270 %       I N D E X
 271 %
 272 \cleardoublepage
 273 \refstepcounter{pdfdummy}
 274
 275 \ifthenelse{\equal{\gmxlite}{1}}{}{
 276 \addcontentsline{toc}{chapter}{Index}
 277
 278 \renewcommand{\see}[2]{\mbox{} \mbox{\textit{see} #1}}
 279 \printindex
 280 } % Brace matches ifthenelse test for gmxlite
 281
 282 \end{document}
 283
 284 % LocalWords:  Groningen der Spoel Lindahl Nijenborgh Carsten Kutzner Aldert
 285 % LocalWords:  Buuren Apol Meulenhoff Tieleman Sijbers Feenstra Rudi Drunen Sij
 286 % LocalWords:  Berendsen pretention bers ser anual Uppsala Mainz unpubl
 287 % LocalWords:  Bioinformatics GROMACS Rossen Apostolov ar Bjelkmar
 288 % LocalWords:  Fritsch Gerrit Groenhof Junghans Kasson Larsson Peiter
 289 % LocalWords:  Teemu Murtola Szil ard Pronk Jochen Lambeth Lemkul
 290 % LocalWords:  Marklund Maarten