g_dyecoupl - extracts dye dynamics from trajectories
VERSION 4.6.3
g_dyecoupl −f traj.xtc −n index.ndx −ot rkappa.xvg −oe insteff.xvg −o rkappa.dat −rhist rhist.xvg −khist khist.xvg −[no]h −[no]version −nice int −b time −e time −tu enum −[no]w −xvg enum −[no]pbcdist −[no]norm −bins int −R0 real
This tool 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.
−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
−[no]hno
Print help info and quit
−[no]versionno
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]wno
View output .xvg, .xpm, .eps and .pdb files
−xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
−[no]pbcdistno
Distance R based on PBC
−[no]normno
Normalize histograms
−bins int 50
of histogram bins
−R0 real −1
Foerster radius including kappa2=2/3 in nm
More information about GROMACS is available at <http://www.gromacs.org/>.