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)