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g_dyecouplMain Table of Contents |
VERSION 4.6.3
Fri 5 Jul 2013
| VERSION 4.6.3 |
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.
| 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 |
| 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 |