Main Table of Contents

Wed 13 Nov 2013


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.


-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

-[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