gmx-dyecoupl1
Extract dye dynamics from trajectories
Usage
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>]
Overview
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)
|
Trajectory: xtc trr cpt gro g96 pdb tng |
|---|---|
-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)
|
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 |
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.