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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 di- pole 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/...>] (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 2025, GROMACS development team 2025.0 Feb 10, 2025 GMX-DYECOUPL(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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