gromacs.tex

% This file is part of the GROMACS molecular simulation package.
%
% Copyright (c) 2013, by the GROMACS development team, led by
% David van der Spoel, Berk Hess, Erik Lindahl, and including many
% others, as listed in the AUTHORS file in the top-level source
% directory and at http://www.gromacs.org.
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% derived work must not be called official GROMACS. Details are found
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% To help us fund GROMACS development, we humbly ask that you cite
% the research papers on the package. Check out http://www.gromacs.org

\documentclass[11pt,a4paper,twoside]{gmxmanual}
\usepackage{here,picins,fancy,array,tabularx,multicol,dcolumn,makeidx,times,ifthen,enumitem,longtable,pdflscape}
%citesort was old, deprecated in tex, and doesn't work with hyperref/pdftex.
%it is rumored you could achieve the same functionality with natbib, but
%after a couple of hours of trial I gave up... /EL
\input{macros}

% If you set gmxlite to 1 a very much shortened version of the manual 
% will be generated, which may be useful for teaching.
\newcommand{\gmxlite}{0}

\begin{document}

%roman pagenumbers for the preamble stuff
\pagenumbering{roman}

% Adjust margins on front page to make it
% symmetrical. It is reset on the next page.
\addtolength{\oddsidemargin}{-5mm}

%
%       F R O N T P A G E       
%
\pagestyle{empty}
\begin{center}

\textcolor{blue}{\fontsize{84}{96} \selectfont GROMACS}
\vspace{4mm}

\textcolor{blue}{\LARGE \em Groningen Machine for Chemical Simulations}
\vspace{4mm}

\includegraphics[height=5in]{plots/peregrine}
\vspace{4mm}

\ifthenelse{\equal{\gmxlite}{1}}
{
\fcolorbox{blue}{blue}{\textcolor{white}{\fontsize{56}{64} \selectfont User Manual {\em ~Lite~}}}
}
{
\fcolorbox{blue}{blue}{\textcolor{white}{\fontsize{56}{64} \selectfont ~USER MANUAL~}}
} % Brace matches ifthenelse test for gmxlite
\vspace{4mm}

\textcolor{blue}{\fontsize{48}{56} \selectfont ~Version \gmxver~}


%\vspace{0.25cm}
%{\fontsize{30}{36} \selectfont \bf Version \gmxver}

\end{center}
\vfill

\ifthenelse{\equal{\gmxlite}{1}} 
{
\newpage
{\bf
This text is a shortened version of the full {\gromacs} manual, written
by David van der Spoel, Berk Hess, Erik Lindahl and others. Please
find further information on our website {\wwwpage}.}

\vspace{2cm}

\noindent \copyright\ 1991--2000: 
Department of Biophysical Chemistry, University of Groningen. 
Nijenborgh 4, 9747 AG Groningen, The Netherlands.\\
\medskip

\noindent \copyright\ 2001--{\gmxyear}:
The {\gromacs} development teams at the Royal Institute of Technology and \\
Uppsala University, Sweden.
} 
{ 
\cleardoublepage
} % Brace matches ifthenelse test for gmxlite
%reset to normal margins
\addtolength{\oddsidemargin}{5mm}

%
%       P R E F A C E
%
\renewcommand{\chaptermark}[1]{\markboth{#1}{#1}} % remember chapter title
\renewcommand{\sectionmark}[1]{\markright{\thesection\ #1}}
                                                % section number and title
\lhead[\fancyplain{}{\em\thepage}]{\fancyplain{}{\em\rightmark}}
\rhead[\fancyplain{}{\em\leftmark}]{\fancyplain{}{\em\thepage}}
\cfoot{}

\ifthenelse{\equal{\gmxlite}{1}}{}{
\begin{center}
\phantom{ }
\vspace{1cm}
{\fontsize{40}{50} \selectfont 
GROMACS\\
USER MANUAL\\[1cm]
}
{\LARGE\bf Version \gmxver}\\[1cm]

{\Large 
Contributions from \\
\vspace{5mm}

Mark Abraham, Emile Apol, Rossen Apostolov, \\
Herman J.C. Berendsen, Aldert van Buuren, P\"ar Bjelkmar, \\
Rudi van Drunen, Anton Feenstra, Sebastian Fritsch, \\
Gerrit Groenhof, Christoph Junghans, Jochen Hub, Peter Kasson, \\
Carsten Kutzner, Brad Lambeth, Per Larsson, Justin A. Lemkul, \\
Erik Marklund, Peiter Meulenhoff, Teemu Murtola, \\
Szil\'ard P\'all, Sander Pronk, Roland Schulz, \\
Michael Shirts, Alfons Sijbers, Peter Tieleman and Maarten Wolf. \\}
\vspace{5mm}

{\LARGE Berk Hess, David van der Spoel, and Erik Lindahl.}
\vspace{10mm}
\end{center}

\vfill


\noindent \copyright\ 1991--2000: 
Department of Biophysical Chemistry, University of Groningen. \\
Nijenborgh 4, 9747 AG Groningen, The Netherlands.\\
\medskip

\noindent \copyright\ 2001--{\gmxyear}:
The {\gromacs} development teams at the Royal Institute of Technology and \\
Uppsala University, Sweden.

\vspace{5mm}

More information can be found on our website: {\wwwpage}.


\newpage
\pagestyle{fancyplain}

\subsection*{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}, or to
one of the mailing lists (see \wwwpage).

We try to release an updated version of the manual whenever
we release a new version of the software, 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. 

\subsection*{On-line Resources}
You can find more documentation and other material at our homepage
\wwwpage. Among other things there is an on-line reference, several
{\gromacs} mailing lists with archives and contributed
topologies/force fields.

\subsection*{Citation information}
When \normindex{citing} this document in any scientific publication
please refer to it as:
\begin{quote}
\raggedright
D. van der Spoel, E. Lindahl, B. Hess, and the GROMACS development team,
\hspace{0.3em} {\em {\gromacs} {U}ser {M}anual version \gmxver},
\hspace{0.3em} {\wwwpage} ({\gmxyear})
\end{quote}
However, we prefer that you cite (some of) the {\gromacs}
papers~\cite{Bekker93a,Berendsen95a,Lindahl2001a,Spoel2005a,Hess2008b} when you publish
your results. Any future development depends on academic research
grants, since the package is distributed as free software!

\subsection*{Current development}
{\gromacs} is a joint effort, with contributions from lots of developers around
the world. The core development is currently taking place at
\begin{itemize}
\item Department of Cellular and Molecular Biology, Uppsala University, Sweden.\\ 
(David van der Spoel).
\item Stockholm Bioinformatics Center, Stockholm University, Sweden \\
(Erik Lindahl).
\item Stockholm Bioinformatics Center, Stockholm University, Sweden \\
(Berk Hess)
\end{itemize}

\subsection*{{\gromacs} is {\em Free Software}}
The entire {\gromacs} package is available under the GNU Lesser
General Public License, version 2.1. 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
\href{http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html}{http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html}.

The {\gromacs} source code and and selected set of binary packages are
available on our homepage, \wwwpage. Have fun.
} % Brace matches ifthenelse test for gmxlite

\newpage
%       C O N T E N T S
%
\tableofcontents
%\listoffigures
%\listoftables

%
%       R E A L   M A N U A L
%
\cleardoublepage
\pagenumbering{arabic}

\include{intro}
\include{defunits}
\include{algorithms}
\include{forcefield}

\ifthenelse{\equal{\gmxlite}{1}}{}{
\include{topology}
\include{special}
\include{programs}
} % Brace matches ifthenelse test for gmxlite
\include{analyse}
\ifthenelse{\equal{\gmxlite}{1}}{}{
%
%       A P P E N D I C E S
%
\appendix
\include{install}
\include{implement}
\include{averages}
\include{progman}
} % Brace matches ifthenelse test for gmxlite
%
% The pdfdummy counter is a workaround to get correct
% bookmarks for the index & bibliography in pdf files

\newcounter{pdfdummy}

%
%       B I B L I O G R A P H Y
%
\cleardoublepage
\refstepcounter{pdfdummy}

\addcontentsline{toc}{chapter}{Bibliography}

\bibliographystyle{proteins}
\bibliography{monster,unpubl}

%
%       I N D E X
%
\cleardoublepage
\refstepcounter{pdfdummy}

\ifthenelse{\equal{\gmxlite}{1}}{}{
\addcontentsline{toc}{chapter}{Index}

\renewcommand{\see}[2]{\mbox{} \mbox{\textit{see} #1}}
\printindex
} % Brace matches ifthenelse test for gmxlite

\end{document}

% LocalWords:  Groningen der Spoel Lindahl Nijenborgh Carsten Kutzner Aldert
% LocalWords:  Buuren Apol Meulenhoff Tieleman Sijbers Feenstra Rudi Drunen Sij
% LocalWords:  Berendsen pretention bers ser anual Uppsala Mainz unpubl
% LocalWords:  Bioinformatics GROMACS Rossen Apostolov ar Bjelkmar
% LocalWords:  Fritsch Gerrit Groenhof Junghans Kasson Larsson Peiter
% LocalWords:  Teemu Murtola Szil ard Pronk Jochen Lambeth Lemkul
% LocalWords:  Marklund Maarten