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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 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 multi‐
       ple  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	 peri‐
       odic  boundaries	 in all 3 dimensions. The -norm option (area-) normal‐
       izes 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.gro‐
       macs.org/>.

VERSION 5.0.6						       gmx-dyecoupl(1)

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