gmx-dyecoupl - Extract dye dynamics from trajectories

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                   GMX-DYECOUPL(1)

gmxdyecoupl  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.

       gmx-dyecoupl - Extract dye dynamics from trajectories

       Options to specify input files:

       -f[<.xtc/.trr/...>](traj.xtc)
              Trajectory: xtctrrcptgrog96pdbtng-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

gmx(1)

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

          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>]