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gmx-dyecoupl - Online in the Cloud

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This is the command gmx-dyecoupl that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


gmx-dyecoupl - Extract dye dynamics from trajectories

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)
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)
First frame (ps) to read from trajectory

-e <time> (0)
Last frame (ps) to read from trajectory

-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>
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

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