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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_covar</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_covar</tt> calculates and diagonalizes the (mass-weighted)
  18 covariance matrix.
  19 All structures are fitted to the structure in the structure file.
  20 When this is not a run input file periodicity will not be taken into
  21 account. When the fit and analysis groups are identical and the analysis
  22 is non mass-weighted, the fit will also be non mass-weighted.
  23 <p>
  24 The eigenvectors are written to a trajectory file (<tt>-v</tt>).
  25 When the same atoms are used for the fit and the covariance analysis,
  26 the reference structure for the fit is written first with t=-1.
  27 The average (or reference when <tt>-ref</tt> is used) structure is
  28 written with t=0, the eigenvectors
  29 are written as frames with the eigenvector number as timestamp.
  30 <p>
  31 The eigenvectors can be analyzed with <tt><a href="g_anaeig.html">g_anaeig</a></tt>.
  32 <p>
  33 Option <tt>-ascii</tt> writes the whole covariance matrix to
  34 an ASCII file. The order of the elements is: x1x1, x1y1, x1z1, x1x2, ...
  35 <p>
  36 Option <tt>-<a href="xpm.html">xpm</a></tt> writes the whole covariance matrix to an <a href="xpm.html">xpm</a> file.
  37 <p>
  38 Option <tt>-xpma</tt> writes the atomic covariance matrix to an <a href="xpm.html">xpm</a> file,
  39 i.e. for each atom pair the sum of the xx, yy and zz covariances is
  40 written.
  41 <P>
  42 <H3>Files</H3>
  43 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  44 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  45 <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>
  46 <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>
  47 <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>
  48 <TR><TD ALIGN=RIGHT> <b><tt>-o</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>
  49 <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>
  50 <TR><TD ALIGN=RIGHT> <b><tt>-av</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> average.pdb</a></tt> </TD><TD> Output </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> etc. </TD></TR>
  51 <TR><TD ALIGN=RIGHT> <b><tt>-l</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">   covar.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
  52 <TR><TD ALIGN=RIGHT> <b><tt>-ascii</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">   covar.dat</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic data file </TD></TR>
  53 <TR><TD ALIGN=RIGHT> <b><tt>-xpm</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">   covar.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  54 <TR><TD ALIGN=RIGHT> <b><tt>-xpma</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">  covara.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  55 </TABLE>
  56 <P>
  57 <H3>Other options</H3>
  58 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  59 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  60 <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>
  61 <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>
  62 <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>
  63 <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>
  64 <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>
  65 <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>
  66 <TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
  67 <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>
  68 <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> Fit to a reference structure </TD></TD>
  69 <TR><TD ALIGN=RIGHT> <b><tt>-[no]ref</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Use the deviation from the conformation in the structure file instead of from the average </TD></TD>
  70 <TR><TD ALIGN=RIGHT> <b><tt>-[no]mwa</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Mass-weighted covariance analysis </TD></TD>
  71 <TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Last eigenvector to write away (-1 is till the last) </TD></TD>
  72 <TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Apply corrections for periodic boundary conditions </TD></TD>
  73 </TABLE>
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