gmx dyecoupl

Main Table of Contents VERSION 5.0.7


gmx dyecoupl [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-ot [<.xvg>]]
             [-oe [<.xvg>]] [-o [<.dat>]] [-rhist [<.xvg>]] [-khist [<.xvg>]]
             [-nice ] [-b 


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 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 kappa^2=2/3 in nm