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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_disre</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_disre computes violations of distance restraints.
  18 If necessary all protons can be added to a protein molecule
  19 using the <a href="protonate.html">protonate</a> program.<p>
  20 The program always
  21 computes the instantaneous violations rather than time-averaged,
  22 because this analysis is done from a trajectory file afterwards
  23 it does not make sense to use time averaging. However,
  24 the time averaged values per restraint are given in the <a href="log.html">log</a> file.<p>
  25 An index file may be used to select specific restraints for
  26 printing.<p>
  27 When the optional<tt>-q</tt> flag is given a <a href="pdb.html">pdb</a> file coloured by the
  28 amount of average violations.<p>
  29 When the <tt>-c</tt> option is given, an index file will be read
  30 containing the frames in your trajectory corresponding to the clusters
  31 (defined in another manner) that you want to analyze. For these clusters
  32 the program will compute average violations using the third power
  33 averaging algorithm and print them in the <a href="log.html">log</a> file.
  34 <P>
  35 <H3>Files</H3>
  36 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  37 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  38 <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> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
  39 <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>
  40 <TR><TD ALIGN=RIGHT> <b><tt>-ds</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   drsum.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  41 <TR><TD ALIGN=RIGHT> <b><tt>-da</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  draver.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  42 <TR><TD ALIGN=RIGHT> <b><tt>-dn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   drnum.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  43 <TR><TD ALIGN=RIGHT> <b><tt>-dm</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   drmax.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  44 <TR><TD ALIGN=RIGHT> <b><tt>-dr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   restr.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  45 <TR><TD ALIGN=RIGHT> <b><tt>-l</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">  disres.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
  46 <TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">    viol.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
  47 <TR><TD ALIGN=RIGHT> <b><tt>-q</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html">    viol.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
  48 <TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   clust.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
  49 <TR><TD ALIGN=RIGHT> <b><tt>-x</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">  matrix.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  50 </TABLE>
  51 <P>
  52 <H3>Other options</H3>
  53 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  54 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  55 <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>
  56 <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>
  57 <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>
  58 <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>
  59 <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>
  60 <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>
  61 <TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
  62 <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>
  63 <TR><TD ALIGN=RIGHT> <b><tt>-ntop</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of large violations that are stored in the <a href="log.html">log</a> file every step </TD></TD>
  64 <TR><TD ALIGN=RIGHT> <b><tt>-maxdr</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Maximum distance violation in matrix output. If less than or equal to 0 the maximum will be determined by the data. </TD></TD>
  65 <TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>20</tt> </TD><TD> Number of levels in the matrix output </TD></TD>
  66 <TR><TD ALIGN=RIGHT> <b><tt>-[no]third</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Use inverse third power averaging or linear for matrix output </TD></TD>
  67 </TABLE>
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