The next step is to combine the molecular structure (<TT><a href="gro.html">.gro</a></TT> file),
topology (<TT><a href="top.html">.top</a></TT> file) MD-parameters (<TT><a href="mdp_opt.html">.mdp</a></TT> file) and
(optionally) the
-index file (<TT><a href="ndx.html">ndx</a></TT>) to generate a run input file (<TT><a href="tpr.html">.tpr</a></tt> extension or
-<TT><a href="tpb.html">.tpb</a></tt> if you don't have XDR).
+index file (<TT><a href="ndx.html">ndx</a></TT>) to generate a run input file (<TT><a href="tpr.html">.tpr</a></tt> extension.
This file contains all information needed to start a simulation with GROMACS.
The
<a href="../programs/gmx-grompp.html">gmx grompp</a> program processes all
is the run input file (<TT><a href="tpr.html">.tpr</a></TT> file).
The output files of
<TT><a href="../programs/gmx-mdrun.html">gmx mdrun</a></TT> are the
-trajectory file (<TT><a href="trr.html">.trr</a></TT> file
-or <TT><a href="trj.html">.trj</a></TT> if you don't have XDR) and a logfile (
+trajectory file (<TT><a href="trr.html">.trr</a></TT> file) and a logfile (
<TT><a href="log.html">.log</A></TT> file).
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