---
name: "g_dyecoupl"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "5.0.2-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-dyecoupl"
---

# g\_dyecoupl(1)

Extract dye dynamics from trajectories

Part of [gmx-dyecoupl(1)](/gmx-dyecoupl/1.md).

## 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 \[\<.xvg\>\]\] \[-nice \<int\>\] \[-b \<time\>\] \[-e \<time\>\]\
              \[-tu \<enum\>\] \[-\[no\]w\] \[-xvg \<enum\>\] \[-\[no\]pbcdist\]\
              \[-\[no\]norm\] \[-bins \<int\>\] \[-R0 \<real\>\]

## DESCRIPTION

**gmx dyecoupl** extracts dye dynamics from trajectory files. Currently, R and kappa2 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 kappa2(t), R and kappa2 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 and output files:

**-f** *\[\<.xtc/.trr/...\>\] (traj.xtc) (Input)*\
     Trajectory: xtc trr cpt trj gro g96 pdb tng

**-n** *\[\<.ndx\>\] (index.ndx) (Input)*\
     Index file

**-ot** *\[\<.xvg\>\] (rkappa.xvg) (Output, Optional)*\
     xvgr/xmgr file

**-oe** *\[\<.xvg\>\] (insteff.xvg) (Output, Optional)*\
     xvgr/xmgr file

**-o** *\[\<.dat\>\] (rkappa.dat) (Output, Optional)*\
     Generic data file

**-rhist** *\[\<.xvg\>\] (rhist.xvg) (Output, Optional)*\
     xvgr/xmgr file

**-khist** *\[\<.xvg\>\] (khist.xvg) (Output, Optional)*\
     xvgr/xmgr file

Other options:

**-nice** *\<int\> (19)*\
     Set the nicelevel

**-b** *\<time\> (0)*\
     First frame (ps) to read from trajectory

**-e** *\<time\> (0)*\
     Last frame (ps) to read from trajectory

**-tu** *\<enum\> (ps)*\
     Time unit: 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 kappa2=2/3 in nm

## SEE ALSO

**[gromacs(7)](/gromacs/7.md)**

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