.TH gmx-dyecoupl 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
gmx-dyecoupl \- Extract dye dynamics from trajectories

.SH SYNOPSIS
gmx dyecoupl [\-f [<.xtc/.trr/...>]] [\-n [<.ndx>]] [\-ot [<.xvg>]]
             [\-oe [<.xvg>]] [\-o [<.dat>]] [\-rhist [<.xvg>]]
             [\-khist [<.xvg>]] [\-nice <int>] [\-b <time>] [\-e <time>]
             [\-tu <enum>] [\-[no]w] [\-xvg <enum>] [\-[no]pbcdist]
             [\-[no]norm] [\-bins <int>] [\-R0 <real>]

.SH DESCRIPTION
\fBgmx dyecoupl\fR 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 \fB\-R0\fR). The input dyes have to be whole (see res and mol pbc options in \fBtrjconv\fR). 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 \fB\-pbcdist\fR 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 \fB\-norm\fR option (area\-) normalizes the histograms.

.SH OPTIONS
Options to specify input and output files:

.BI "\-f" " [<.xtc/.trr/...>] (traj.xtc) (Input)"
    Trajectory: xtc trr cpt trj gro g96 pdb tng

.BI "\-n" " [<.ndx>] (index.ndx) (Input)"
    Index file

.BI "\-ot" " [<.xvg>] (rkappa.xvg) (Output, Optional)"
    xvgr/xmgr file

.BI "\-oe" " [<.xvg>] (insteff.xvg) (Output, Optional)"
    xvgr/xmgr file

.BI "\-o" " [<.dat>] (rkappa.dat) (Output, Optional)"
    Generic data file

.BI "\-rhist" " [<.xvg>] (rhist.xvg) (Output, Optional)"
    xvgr/xmgr file

.BI "\-khist" " [<.xvg>] (khist.xvg) (Output, Optional)"
    xvgr/xmgr file


Other options:

.BI "\-nice" " <int> (19)"
    Set the nicelevel

.BI "\-b" " <time> (0)"
    First frame (ps) to read from trajectory

.BI "\-e" " <time> (0)"
    Last frame (ps) to read from trajectory

.BI "\-tu" " <enum> (ps)"
    Time unit: fs, ps, ns, us, ms, s

.BI "\-[no]w" "  (no)"
    View output \fB.xvg\fR, \fB.xpm\fR, \fB.eps\fR and \fB.pdb\fR files

.BI "\-xvg" " <enum> (xmgrace)"
    xvg plot formatting: xmgrace, xmgr, none

.BI "\-[no]pbcdist" "  (no)"
    Distance R based on PBC

.BI "\-[no]norm" "  (no)"
    Normalize histograms

.BI "\-bins" " <int> (50)"
    of histogram bins

.BI "\-R0" " <real> (-1)"
    Foerster radius including kappa2=2/3 in nm


.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.