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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:

Trajectory: xtc trr cpt gro g96 pdb tng
Index file

Options to specify output files:

Other options:

Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Unit for time values: fs, ps, ns, us, ms, s
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr, none
-[no]pbcdist (no)
Distance R based on PBC
-[no]norm (no)
Normalize histograms
# of histogram bins
Foerster radius including kappa^2=2/3 in nm



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2021, GROMACS development team

March 29, 2021 2020.6-Debian-2020.6-2