manual/programs.tex

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  33
  34 \chapter{Run parameters and Programs}
  35 \label{ch:programs}
  36
  37 \section{On-line and HTML manuals}
  38 \index{online manual}
  39 \index{html manual}
  40 % TODO Check that these statements and default file locations are
  41 % current when the help-writing module has stabilized
  42 All the information in this chapter can also be found in HTML
  43 format in your {\gromacs} data directory. The path depends on
  44 where your files are installed, but the default location is
  45 {\tt /usr/local/gromacs/share/gromacs/html/online.html}.
  46 If you installed from Linux packages it can typically be found as
  47 {\tt /usr/share/gromacs/html/online.html}.
  48 You can also use the online manual from the {\gromacs} web site,
  49 \url{http://manual.gromacs.org/current}.
  50
  51 In addition, we install standard UNIX man pages for all the programs. If
  52 you have sourced the {\tt GMXRC} script in the {\gromacs} binary directory for
  53 your host they should already be present in your {\tt MANPATH} environment variable, and you
  54 should be able to type {\eg} {\tt man gmx-grompp}. You can also use
  55 the {\tt -h} flag on the command line (e.g. {\tt gmx grompp -h}) to
  56 see the same information, as well as {\tt gmx help grompp}.
  57 The list of all programs are available from {\tt gmx help}.
  58
  59 \section{File types\swapindexquiet{file}{type}}
  60 \label{sec:fileformats}
  61 \tabref{form} lists the file types used by {\gromacs} along with
  62 a short description, and you can find a more detail description for
  63 each file in your HTML reference, or in our online version.
  64
  65 {\gromacs} files written in \normindex{XDR} format can be read on any
  66 architecture with {\gromacs} version 1.6 or later if the configuration
  67 script found the XDR libraries on your system. They should always be
  68 present on UNIX since they are necessary for NFS support.
  69
  70 \input{files}
  71
  72 \section{Run Parameters\swapindexquiet{run}{parameter}}
  73 \input{mdp_opt}
  74
  75 % LocalWords:  online html GMXRC MANPATH grompp xdr NFS