| ## g_dyecoupl Main Table of Contents | VERSION 4.6 Sat 19 Jan 2013

### Description

This tool 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.

### Files

option | filename | type | description
--- | --- | --- | ---
`-f` | `traj.xtc` | Input | Trajectory: xtc trr trj gro g96 pdb cpt
`-n` | `index.ndx` | Input | Index file
`-ot` | `rkappa.xvg` | Output, Opt. | xvgr/xmgr file
`-oe` | `insteff.xvg` | Output, Opt. | xvgr/xmgr file
`-o` | `rkappa.dat` | Output, Opt. | Generic data file
`-rhist` | `rhist.xvg` | Output, Opt. | xvgr/xmgr file
`-khist` | `khist.xvg` | Output, Opt. | xvgr/xmgr file

### Other options

option | type | default | description
--- | --- | --- | ---
`-[no]h` | bool | `no` | Print help info and quit
`-[no]version` | bool | `no` | Print version info and quit
`-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` or `s`
`-[no]w` | bool | `no` | View output `.xvg`, `.xpm`, `.eps` and `.pdb` files
`-xvg` | enum | `xmgrace` | xvg plot formatting: `xmgrace`, `xmgr` or `none`
`-[no]pbcdist` | bool | `no` | Distance R based on PBC
`-[no]norm` | bool | `no` | Normalize histograms
`-bins` | int | `50` | # of histogram bins
`-R0` | real | `-1` | Foerster radius including kappa^2=2/3 in nm

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