NAME

       g_dyecoupl - extracts dye dynamics from trajectories

       VERSION 4.6.5

SYNOPSIS

       g_dyecoupl  -f traj.xtc -n index.ndx -ot rkappa.xvg -oe insteff.xvg -o rkappa.dat -rhist rhist.xvg -khist
       khist.xvg -[no]h -[no]version -nice int -b time -e time -tu enum -[no]w -xvg enum -[no]pbcdist  -[no]norm
       -bins int -R0 real

DESCRIPTION

       This tool extracts dye dynamics from trajectory files.  Currently, R and kappa2 between dyes is extracted
       for (F)RET simulations with assumed dipolar coupling as in the Foerster equation.  It further allows  the
       calculation  of  R(t)  and  kappa2(t), R and kappa2 histograms and averages, as well as the instantaneous
       FRET efficiency E(t) for a specified Foerster radius R_0 (switch  -R0).  The input dyes have to be  whole
       (see  res  and  mol  pbc  options in  trjconv).  The dye transition dipole moment has to be defined by at
       least a single atom pair, however multiple atom pairs can be provided in the index file. The  distance  R
       is  calculated  on  the  basis  of  the  COMs  of  the given atom pairs.  The  -pbcdist option calculates
       distances to the nearest periodic image instead to the distance in the box. This works  however  only,for
       periodic boundaries in all 3 dimensions.  The  -norm option (area-) normalizes the histograms.

FILES

       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -n index.ndx Input
        Index file

       -ot rkappa.xvg Output, Opt.
        xvgr/xmgr file

       -oe insteff.xvg Output, Opt.
        xvgr/xmgr file

       -o rkappa.dat Output, Opt.
        Generic data file

       -rhist rhist.xvg Output, Opt.
        xvgr/xmgr file

       -khist khist.xvg Output, Opt.
        xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -nice int 19
        Set the nicelevel

       -b time 0
        First frame (ps) to read from trajectory

       -e time 0
        Last frame (ps) to read from trajectory

       -tu enum ps
        Time unit:  fs,  ps,  ns,  us,  ms or  s

       -[no]wno
        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -[no]pbcdistno
        Distance R based on PBC

       -[no]normno
        Normalize histograms

       -bins int 50
         of histogram bins

       -R0 real -1
        Foerster radius including kappa2=2/3 in nm

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

                                                 Mon 2 Dec 2013                                    g_dyecoupl(1)