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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_mdmat</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>
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  15 <H3>Description</H3>
  16 <p>
  17 g_mdmat makes distance matrices consisting of the smallest distance
  18 between residue pairs. With -frames these distance matrices can be
  19 stored as a function
  20 of time, to be able to see differences in tertiary structure as a
  21 funcion of time. If you choose your options unwise, this may generate
  22 a large output file. Default only an averaged matrix over the whole
  23 trajectory is output.
  24 Also a count of the number of different atomic contacts between
  25 residues over the whole trajectory can be made.
  26 The output can be processed with <a href="xpm2ps.html">xpm2ps</a> to make a PostScript (tm) plot.
  27 <P>
  28 <H3>Files</H3>
  29 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  30 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></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 </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>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
  33 <TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
  34 <TR><TD ALIGN=RIGHT> <b><tt>-mean</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">      dm.xpm</a></tt> </TD><TD> Output </TD><TD> X PixMap compatible matrix file </TD></TR>
  35 <TR><TD ALIGN=RIGHT> <b><tt>-frames</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">     dmf.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  36 <TR><TD ALIGN=RIGHT> <b><tt>-no</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">     num.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </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>19</tt> </TD><TD> Set the nicelevel </TD></TD>
  45 <TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
  46 <TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
  47 <TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
  48 <TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
  49 <TR><TD ALIGN=RIGHT> <b><tt>-t</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1.5   </tt> </TD><TD> trunc distance </TD></TD>
  50 <TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>40</tt> </TD><TD> Discretize distance in # levels </TD></TD>
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