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gmx-dyecoupl - Extract dye dynamics from trajectories


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>]


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 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)
First frame (ps) to read from trajectory

-e <time> (0)
Last frame (ps) to read from trajectory

-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>
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

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