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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_morph</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_morph does a linear interpolation of conformations in order to
  18 create intermediates. Of course these are completely unphysical, but
  19 that you may try to justify yourself. Output is in the form of a
  20 generic trajectory. The number of intermediates can be controlled with
  21 the -ninterm flag. The first and last flag correspond to the way of
  22 interpolating: 0 corresponds to input structure 1 while
  23 1 corresponds to input structure 2.
  24 If you specify first &lt; 0 or last &gt; 1 extrapolation will be
  25 on the path from input structure x1 to x2. In general the coordinates
  26 of the intermediate x(i) out of N total intermidates correspond to:<p>
  27 x(i) = x1 + (first+(i/(N-1))*(last-first))*(x2-x1)<p>
  28 Finally the RMSD with respect to both input structures can be computed
  29 if explicitly selected (-or option). In that case an index file may be
  30 read to select what group RMS is computed from.
  31 <P>
  32 <H3>Files</H3>
  33 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  34 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  35 <TR><TD ALIGN=RIGHT> <b><tt>-f1</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   conf1.gro</a></tt> </TD><TD> Input </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> etc. </TD></TR>
  36 <TR><TD ALIGN=RIGHT> <b><tt>-f2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   conf2.gro</a></tt> </TD><TD> Input </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> etc. </TD></TR>
  37 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">  interm.xtc</a></tt> </TD><TD> Output </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>
  38 <TR><TD ALIGN=RIGHT> <b><tt>-or</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">rms-interm.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  39 <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>
  40 </TABLE>
  41 <P>
  42 <H3>Other options</H3>
  43 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  44 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  45 <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>
  46 <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>
  47 <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>
  48 <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>
  49 <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>
  50 <TR><TD ALIGN=RIGHT> <b><tt>-ninterm</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>11</tt> </TD><TD> Number of intermediates </TD></TD>
  51 <TR><TD ALIGN=RIGHT> <b><tt>-first</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Corresponds to first generated structure (0 is input x0, see above) </TD></TD>
  52 <TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1     </tt> </TD><TD> Corresponds to last generated structure (1 is input x1, see above) </TD></TD>
  53 <TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Do a least squares fit of the second to the first structure before interpolating </TD></TD>
  54 </TABLE>
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