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GMX-DYECOUPL(1) GROMACS GMX-DYECOUPL(1)

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)
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/>.

2022, GROMACS development team
January 14, 2022 2021.5
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