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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dih</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_dih can do two things. The default is to analyze dihedral transitions
  18 by merely computing all the dihedral angles defined in your topology
  19 for the whole trajectory. When a dihedral flips over to another minimum
  20 an angle/time plot is made.<p>
  21 The opther option is to discretize the dihedral space into a number of
  22 bins, and group each conformation in dihedral space in the
  23 appropriate bin. The output is then given as a number of dihedral
  24 conformations sorted according to occupancy.
  25 <P>
  26 <H3>Files</H3>
  27 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  28 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  29 <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>
  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 </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>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="out.html">   hello.out</a></tt> </TD><TD> Output </TD><TD> Generic output file </TD></TR>
  32 </TABLE>
  33 <P>
  34 <H3>Other options</H3>
  35 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  36 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  37 <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>
  38 <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>
  39 <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>
  40 <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>
  41 <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>
  42 <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>
  43 <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>
  44 <TR><TD ALIGN=RIGHT> <b><tt>-[no]sa</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Perform cluster analysis in dihedral space instead of analysing dihedral transitions. </TD></TD>
  45 <TR><TD ALIGN=RIGHT> <b><tt>-mult</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> mulitiplicity for dihedral angles (by default read from topology) </TD></TD>
  46 </TABLE>
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