programs.tex

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\chapter{Run parameters and Programs}
\label{ch:programs}

\section{On-line and HTML manuals}
\index{online manual}
\index{html manual}
All the information in this chapter can also be found in HTML
format in your {\gromacs} data directory. The path depends on
where your files are installed, but the default location is \\
\centerline{\tt /usr/local/gromacs/share/html/online.html}
Or, if you installed from Linux packages it can be found as\\
\centerline{\tt /usr/local/share/gromacs/html/online.html}
You can also use the online from our web site,\\
\centerline{\href{http://manual.gromacs.org/current/}{http://manual.gromacs.org/current/}}

In addition, we install standard UNIX manuals for all the programs. If
you have sourced the {\tt GMXRC} script in the {\gromacs} binary directory for
your host they should already be present in your {\tt \$MANPATH}, and you
should be able to type {\eg} {\tt man grompp}.

The program manual pages can also be found in
\appref{progman} in this manual.

\section{File types\swapindexquiet{file}{type}}
\label{sec:fileformats}
\tabref{form} lists the file types used by {\gromacs} along with
a short description, and you can find a more detail description for
each file in your HTML reference, or in our online version.

{\gromacs} files written in \normindex{XDR} format can be read on any
architecture with {\gromacs} version 1.6 or later if the configuration
script found the XDR libraries on your system. They should always be
present on UNIX since they are necessary for NFS support.

\input{files}

\section{Run Parameters\swapindexquiet{run}{parameter}}
\input{mdp_opt}

\section{Programs by topic\index{programs by topic}}
\input{proglist}

% LocalWords:  online html GMXRC MANPATH grompp progman xdr NFS