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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 4.6<br>
  13 Sat 19 Jan 2013</B></td></tr></TABLE>
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  15 <H3>Description</H3>
  16 <p>
  17 <tt>g_morph</tt> 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 <tt>-ninterm</tt> 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 <tt>-first</tt> &lt; 0 or <tt>-last</tt> &gt; 1 extrapolation will be
  25 on the path from input structure x_1 to x_2. In general, the coordinates
  26 of the intermediate x(i) out of N total intermediates correspond to:<p>
  27 x(i) = x_1 + (first+(i/(N-1))*(last-first))*(x_2-x_1)<p>
  28 Finally the RMSD with respect to both input structures can be computed
  29 if explicitly selected (<tt>-or</tt> option). In that case, an index file may be
  30 read to select the group from which the RMS is computed.
  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> 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> 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> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> 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 x_1, 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 x_2, see above) </TD></TD>
  53 <TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> 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>
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