---
name: "gmx-dyecoupl"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "2025.2-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-dyecoupl"
---

# gmx-dyecoupl(1)

Extract dye dynamics from trajectories

## 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 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

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)](/gmx/1.md)**

More information about GROMACS is available at \<*http://www.gromacs.org/*\>.

## COPYRIGHT

2025, GROMACS development team