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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_nmeig</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_nmeig calculates the eigenvectors/values of a (Hessian) matrix,
  18 which can be calculated with <tt><a href="mdrun.html">mdrun</a></tt>.
  19 The eigenvectors are written to a trajectory file (<tt>-v</tt>).
  20 The structure is written first with t=0. The eigenvectors
  21 are written as frames with the eigenvector number as timestamp.
  22 The eigenvectors can be analyzed with <tt><a href="g_anaeig.html">g_anaeig</a></tt>.
  23 An ensemble of structures can be generated from the eigenvectors with
  24 <tt><a href="g_nmens.html">g_nmens</a></tt>. When mass weighting is used, the generated eigenvectors
  25 will be scaled back to plain cartesian coordinates before generating the
  26 output - in this case they will no longer be exactly orthogonal in the
  27 standard cartesian norm (But in the mass weighted norm they would be).
  28 <P>
  29 <H3>Files</H3>
  30 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  31 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  32 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mtx.html"> hessian.mtx</a></tt> </TD><TD> Input </TD><TD> Hessian matrix </TD></TR>
  33 <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>
  34 <TR><TD ALIGN=RIGHT> <b><tt>-of</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">eigenfreq.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  35 <TR><TD ALIGN=RIGHT> <b><tt>-ol</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">eigenval.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </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> Output </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
  37 </TABLE>
  38 <P>
  39 <H3>Other options</H3>
  40 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  41 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  42 <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>
  43 <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>
  44 <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>
  45 <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>
  46 <TR><TD ALIGN=RIGHT> <b><tt>-[no]m</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Divide elements of Hessian by product of sqrt(mass) of involved atoms prior to diagonalization. This should be used for 'Normal Modes' analysis </TD></TD>
  47 <TR><TD ALIGN=RIGHT> <b><tt>-first</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> First eigenvector to write away </TD></TD>
  48 <TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>50</tt> </TD><TD> Last eigenvector to write away </TD></TD>
  49 </TABLE>
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