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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 4.6<br>
  13 Sat 19 Jan 2013</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 <tt>.<a href="xpm.html">xpm</a></tt> file.
  37 <p>
  38 Option <tt>-xpma</tt> writes the atomic covariance matrix to an <tt>.<a href="xpm.html">xpm</a></tt> file,
  39 i.e. for each atom pair the sum of the xx, yy and zz covariances is
  40 written.
  41 <p>
  42 Note that the diagonalization of a matrix requires memory and time
  43 that will increase at least as fast as than the square of the number
  44 of atoms involved. It is easy to run out of memory, in which
  45 case this tool will probably exit with a 'Segmentation fault'. You
  46 should consider carefully whether a reduced set of atoms will meet
  47 your needs for lower costs.
  48 <P>
  49 <H3>Files</H3>
  50 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  51 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  52 <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>
  53 <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>
  54 <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>
  55 <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>
  56 <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>
  57 <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>
  58 <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>
  59 <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>
  60 <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>
  61 <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>
  62 </TABLE>
  63 <P>
  64 <H3>Other options</H3>
  65 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  66 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  67 <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>
  68 <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>
  69 <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>
  70 <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>
  71 <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>
  72 <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>
  73 <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>
  74 <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>
  75 <TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Fit to a reference structure </TD></TD>
  76 <TR><TD ALIGN=RIGHT> <b><tt>-[no]ref</tt></b> </TD><TD ALIGN=RIGHT> 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>
  77 <TR><TD ALIGN=RIGHT> <b><tt>-[no]mwa</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Mass-weighted covariance analysis </TD></TD>
  78 <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>
  79 <TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Apply corrections for periodic boundary conditions </TD></TD>
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