gmx dyecoupl¶
Synopsis¶
gmx dyecoupl [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-ot [<.xvg>]]
[-oe [<.xvg>]] [-o [<.dat>]] [-rhist [<.xvg>]]
[-khist [<.xvg>]] [-b <time>] [-e <time>] [-tu <enum>]
[-[no]w] [-xvg <enum>] [-[no]pbcdist] [-[no]norm]
[-bins <int>] [-R0 <real>]
Description¶
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¶
Options to specify input files:
-f[<.xtc/.trr/…>] (traj.xtc)-n[<.ndx>] (index.ndx)Index file
Options to specify output files:
-ot[<.xvg>] (rkappa.xvg) (Optional)xvgr/xmgr file
-oe[<.xvg>] (insteff.xvg) (Optional)xvgr/xmgr file
-o[<.dat>] (rkappa.dat) (Optional)Generic data file
-rhist[<.xvg>] (rhist.xvg) (Optional)xvgr/xmgr file
-khist[<.xvg>] (khist.xvg) (Optional)xvgr/xmgr file
Other options:
-b<time> (0)Time of first frame to read from trajectory (default unit ps)
-e<time> (0)Time of last frame to read from trajectory (default unit ps)
-tu<enum> (ps)Unit for time values: fs, ps, ns, us, ms, s
-[no]w(no)-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