g_dyecoupl(1)

NAME
g_dyecoupl - extracts dye dynamics from trajectories VERSION 4.6.3

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/>.