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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dyecoupl</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>
  14 <HR>
  15 <H3>Description</H3>
  16 <p>
  17 This tool extracts dye dynamics from trajectory files.
  18 Currently, R and kappa^2 between dyes is extracted for (F)RET
  19 simulations with assumed dipolar coupling as in the Foerster equation.
  20 It further allows the calculation of R(t) and kappa^2(t), R and
  21 kappa^2 histograms and averages, as well as the instantaneous FRET
  22 efficiency E(t) for a specified Foerster radius R_0 (switch <tt>-R0</tt>).
  23 The input dyes have to be whole (see res and mol pbc options
  24 in <tt><a href="trjconv.html">trjconv</a></tt>).
  25 The dye transition dipole moment has to be defined by at least
  26 a single atom pair, however multiple atom pairs can be provided
  27 in the index file. The distance R is calculated on the basis of
  28 the COMs of the given atom pairs.
  29 The <tt>-pbcdist</tt> option calculates distances to the nearest periodic
  30 image instead to the distance in the box. This works however only,for periodic boundaries in all 3 dimensions.
  31 The <tt>-norm</tt> option (area-) normalizes the histograms.
  32 <P>
  33 <H3>Files</H3>
  34 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  35 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  36 <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>
  37 <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 </TD><TD> Index file </TD></TR>
  38 <TR><TD ALIGN=RIGHT> <b><tt>-ot</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  rkappa.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  39 <TR><TD ALIGN=RIGHT> <b><tt>-oe</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> insteff.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  40 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">  rkappa.dat</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic data file </TD></TR>
  41 <TR><TD ALIGN=RIGHT> <b><tt>-rhist</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   rhist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  42 <TR><TD ALIGN=RIGHT> <b><tt>-khist</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   khist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  43 </TABLE>
  44 <P>
  45 <H3>Other options</H3>
  46 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  47 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  48 <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>
  49 <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>
  50 <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>
  51 <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>
  52 <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>
  53 <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>
  54 <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>
  55 <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>
  56 <TR><TD ALIGN=RIGHT> <b><tt>-[no]pbcdist</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Distance R based on PBC </TD></TD>
  57 <TR><TD ALIGN=RIGHT> <b><tt>-[no]norm</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Normalize histograms </TD></TD>
  58 <TR><TD ALIGN=RIGHT> <b><tt>-bins</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>50</tt> </TD><TD> # of histogram bins </TD></TD>
  59 <TR><TD ALIGN=RIGHT> <b><tt>-R0</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> Foerster radius including kappa^2=2/3 in nm </TD></TD>
  60 </TABLE>
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