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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_nmtraj</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 <tt>g_nmtraj</tt> generates an virtual trajectory from an eigenvector,
  18 corresponding to a harmonic cartesian oscillation around the average
  19 structure. The eigenvectors should normally be mass-weighted, but you can
  20 use non-weighted eigenvectors to generate orthogonal motions.
  21 The output frames are written as a trajectory file covering an entire period, and
  22 the first frame is the average structure. If you write the trajectory in (or convert to)
  23 PDB format you can view it directly in PyMol and also render a photorealistic movie.
  24 Motion amplitudes are calculated from the eigenvalues and a preset temperature,
  25 assuming equipartition of the energy over all modes. To make the motion clearly visible
  26 in PyMol you might want to amplify it by setting an unrealistic high temperature.
  27 However, be aware that both the linear cartesian displacements and mass weighting will
  28 lead to serious structure deformation for high amplitudes - this is is simply a limitation
  29 of the cartesian normal mode model. By default the selected eigenvector is set to 7, since
  30  the first six normal modes are the translational and rotational degrees of freedom.
  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>-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>
  36 <TR><TD ALIGN=RIGHT> <b><tt>-v</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec.trr</a></tt> </TD><TD> Input </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
  37 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">  nmtraj.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> </TD></TR>
  38 </TABLE>
  39 <P>
  40 <H3>Other options</H3>
  41 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  42 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  43 <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>
  44 <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>
  45 <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>
  46 <TR><TD ALIGN=RIGHT> <b><tt>-eignr</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>7</tt> </TD><TD> String of eigenvectors to use (first is 1) </TD></TD>
  47 <TR><TD ALIGN=RIGHT> <b><tt>-phases</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>0.0</tt> </TD><TD> String of phases (default is 0.0) </TD></TD>
  48 <TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>300   </tt> </TD><TD> Temperature in Kelvin </TD></TD>
  49 <TR><TD ALIGN=RIGHT> <b><tt>-amplitude</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.25  </tt> </TD><TD> Amplitude for modes with eigenvalue&lt;=0 </TD></TD>
  50 <TR><TD ALIGN=RIGHT> <b><tt>-nframes</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>30</tt> </TD><TD> Number of frames to generate </TD></TD>
  51 </TABLE>
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