.. _gmx rotacf:

gmx rotacf
==========

Synopsis
--------

.. parsed-literal::

    gmx rotacf [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr>]`] [:strong:`-n` :emphasis:`[<.ndx>]`]
               [:strong:`-o` :emphasis:`[<.xvg>]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`] [:strong:`-dt` :emphasis:`<time>`]
               [:strong:`-[no]w`] [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-[no]d`] [:strong:`-[no]aver`]
               [:strong:`-acflen` :emphasis:`<int>`] [:strong:`-[no]normalize`] [:strong:`-P` :emphasis:`<enum>`]
               [:strong:`-fitfn` :emphasis:`<enum>`] [:strong:`-beginfit` :emphasis:`<real>`] [:strong:`-endfit` :emphasis:`<real>`]

Description
-----------

``gmx rotacf`` calculates the rotational correlation function
for molecules. Atom triplets (i,j,k) must be given in the index
file, defining two vectors ij and jk. The rotational ACF
is calculated as the autocorrelation function of the vector
n = ij x jk, i.e. the cross product of the two vectors.
Since three atoms span a plane, the order of the three atoms
does not matter. Optionally, by invoking the ``-d`` switch, you can
calculate the rotational correlation function for linear molecules
by specifying atom pairs (i,j) in the index file.

EXAMPLES

``gmx rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1
-fa expfit-x-P1 -beginfit 2.5 -endfit 20.0``

This will calculate the rotational correlation function using a first
order Legendre polynomial of the angle of a vector defined by the index
file. The correlation function will be fitted from 2.5 ps until 20.0 ps
to a two-parameter exponential.

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`
``-s`` [<.tpr>] (topol.tpr)
    Portable xdr run input file
``-n`` [<.ndx>] (index.ndx)
    Index file

Options to specify output files:

``-o`` [<.xvg>] (rotacf.xvg)
    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)
``-dt`` <time> (0)
    Only use frame when t MOD dt = first time (default unit ps)
``-[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]d``  (no)
    Use index doublets (vectors) for correlation function instead of triplets (planes)
``-[no]aver``  (yes)
    Average over molecules
``-acflen`` <int> (-1)
    Length of the ACF, default is half the number of frames
``-[no]normalize``  (yes)
    Normalize ACF
``-P`` <enum> (0)
    Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3
``-fitfn`` <enum> (none)
    Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
``-beginfit`` <real> (0)
    Time where to begin the exponential fit of the correlation function
``-endfit`` <real> (-1)
    Time where to end the exponential fit of the correlation function, -1 is until the end

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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