docs/manual/programs.tex

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