NAME

       gmx-dyecoupl - Extract dye dynamics from trajectories

SYNOPSIS

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

DESCRIPTION

       gmx  dyecoupl  extracts  dye  dynamics  from  trajectory files.  Currently, R and kappa^2 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 kappa^2(t), R and kappa^2 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.

OPTIONS

       Options to specify input files:

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

       -n [<.ndx>] (index.ndx)
              Index file

       Options to specify output files:

       -ot [<.xvg>] (rkappa.xvg) (Optional)
              xvgr/xmgr file

       -oe [<.xvg>] (insteff.xvg) (Optional)
              xvgr/xmgr file

       -o [<.dat>] (rkappa.dat) (Optional)
              Generic data file

       -rhist [<.xvg>] (rhist.xvg) (Optional)
              xvgr/xmgr file

       -khist [<.xvg>] (khist.xvg) (Optional)
              xvgr/xmgr file

       Other options:

       -b <time> (0)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -tu <enum> (ps)
              Unit for time values: fs, ps, ns, us, ms, s

       -[no]w (no)
              View output .xvg, .xpm, .eps and .pdb files

       -xvg <enum> (xmgrace)
              xvg plot formatting: xmgrace, xmgr, none

       -[no]pbcdist (no)
              Distance R based on PBC

       -[no]norm (no)
              Normalize histograms

       -bins <int> (50)
              # of histogram bins

       -R0 <real> (-1)
              Foerster radius including kappa^2=2/3 in nm

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2024, GROMACS development team

2024.2                                            May 10, 2024                                   GMX-DYECOUPL(1)