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gmx-dyecoupl(1)                 GROMACS Manual                 gmx-dyecoupl(1)

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>]] [-nice <int>] [-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 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.

OPTIONS
       Options to specify input and output files:

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

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

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

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

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

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

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

       Other options:

       -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, 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 kappa2=2/3 in nm

SEE ALSO
       gromacs(7)

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

VERSION 5.0.6                                                  gmx-dyecoupl(1)