| 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:
Options to specify output files:
Other options:
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2023, GROMACS development team
| February 3, 2023 | 2022.5 |