.. _gmx dyecoupl:

gmx dyecoupl
============

Synopsis
--------

.. parsed-literal::

    gmx dyecoupl [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`] [:strong:`-ot` :emphasis:`[<.xvg>]`]
                 [:strong:`-oe` :emphasis:`[<.xvg>]`] [:strong:`-o` :emphasis:`[<.dat>]`] [:strong:`-rhist` :emphasis:`[<.xvg>]`]
                 [:strong:`-khist` :emphasis:`[<.xvg>]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`] [:strong:`-tu` :emphasis:`<enum>`]
                 [:strong:`-[no]w`] [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-[no]pbcdist`] [:strong:`-[no]norm`]
                 [:strong:`-bins` :emphasis:`<int>`] [:strong:`-R0` :emphasis:`<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: :ref:`xtc` :ref:`trr` :ref:`cpt` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`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 :ref:`.xvg <xvg>`, :ref:`.xpm <xpm>`, :ref:`.eps <eps>` and :ref:`.pdb <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

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

   More information about |Gromacs| is available at <http://www.gromacs.org/>.