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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>gmxdump</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
  12 </TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
  13 Thu 26 Aug 2010</B></td></tr></TABLE>
  14 <HR>
  15 <H3>Description</H3>
  16 <p>
  17 gmxdump reads a run input file (<tt>.<a href="tpa.html">tpa</a></tt>/<tt>.<a href="tpr.html">tpr</a></tt>/<tt>.<a href="tpb.html">tpb</a></tt>),
  18 a trajectory (<tt>.<a href="trj.html">trj</a></tt>/<tt>.<a href="trr.html">trr</a></tt>/<tt>.<a href="xtc.html">xtc</a></tt>), an energy
  19 file (<tt>.<a href="ene.html">ene</a></tt>/<tt>.<a href="edr.html">edr</a></tt>), or a checkpoint file (<tt>.cpt</tt>)
  20 and prints that to standard output in a readable format.
  21 This program is essential for checking your run input file in case of
  22 problems.<p>
  23 The program can also preprocess a topology to help finding problems.
  24 Note that currently setting GMXLIB is the only way to customize
  25 directories used for searching include files.
  26 <P>
  27 <H3>Files</H3>
  28 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  29 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  30 <TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
  31 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
  32 <TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edr.html">    ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD> Energy file </TD></TR>
  33 <TR><TD ALIGN=RIGHT> <b><tt>-cp</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="cpt.html">   state.cpt</a></tt> </TD><TD> Input, Opt. </TD><TD> Checkpoint file </TD></TR>
  34 <TR><TD ALIGN=RIGHT> <b><tt>-p</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html">   topol.top</a></tt> </TD><TD> Input, Opt. </TD><TD> Topology file </TD></TR>
  35 <TR><TD ALIGN=RIGHT> <b><tt>-mtx</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mtx.html"> hessian.mtx</a></tt> </TD><TD> Input, Opt. </TD><TD> Hessian matrix </TD></TR>
  36 <TR><TD ALIGN=RIGHT> <b><tt>-om</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mdp.html">  grompp.mdp</a></tt> </TD><TD> Output, Opt. </TD><TD> <a href="grompp.html">grompp</a> input file with MD parameters </TD></TR>
  37 </TABLE>
  38 <P>
  39 <H3>Other options</H3>
  40 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  41 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  42 <TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print help info and quit </TD></TD>
  43 <TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print version info and quit </TD></TD>
  44 <TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
  45 <TR><TD ALIGN=RIGHT> <b><tt>-[no]nr</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology) </TD></TD>
  46 <TR><TD ALIGN=RIGHT> <b><tt>-[no]sys</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> List the atoms and bonded interactions for the whole system instead of for each molecule type </TD></TD>
  47 </TABLE>
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