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GMX-DYECOUPL(1)			    GROMACS		       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_]] [-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  as-
       sumed  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 spec-
       ified 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 in-
       stead 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/^a|>] (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
       2020, GROMACS development team

2020.4				 Oct 06, 2020		       GMX-DYECOUPL(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT

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