.. _gmx velacc:

gmx velacc
==========

Synopsis
--------

.. parsed-literal::

    gmx velacc [:strong:`-f` :emphasis:`[<.trr/.cpt/...>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`]
               [:strong:`-o` :emphasis:`[<.xvg>]`] [:strong:`-os` :emphasis:`[<.xvg>]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`]
               [:strong:`-dt` :emphasis:`<time>`] [:strong:`-[no]w`] [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-[no]m`] [:strong:`-[no]recip`]
               [:strong:`-[no]mol`] [: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 velacc`` computes the velocity autocorrelation function.
When the ``-m`` option is used, the momentum autocorrelation
function is calculated.

With option ``-mol`` the velocity autocorrelation function of
molecules is calculated. In this case the index group should consist
of molecule numbers instead of atom numbers.

By using option ``-os`` you can also extract the estimated
(vibrational) power spectrum, which is the Fourier transform of the
velocity autocorrelation function.
Be sure that your trajectory contains frames with velocity information
(i.e. ``nstvout`` was set in your original :ref:`.mdp <mdp>` file),
and that the time interval between data collection points is
much shorter than the time scale of the autocorrelation.

Options
-------

Options to specify input files:

``-f`` [<.trr/.cpt/...>] (traj.trr)
    Full precision trajectory: :ref:`trr` :ref:`cpt` :ref:`tng`
``-s`` [<.tpr/.gro/...>] (topol.tpr) (Optional)
    Structure+mass(db): :ref:`tpr` :ref:`gro` :ref:`g96` :ref:`pdb` brk ent
``-n`` [<.ndx>] (index.ndx) (Optional)
    Index file

Options to specify output files:

``-o`` [<.xvg>] (vac.xvg)
    xvgr/xmgr file
``-os`` [<.xvg>] (spectrum.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)
``-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]m``  (no)
    Calculate the momentum autocorrelation function
``-[no]recip``  (yes)
    Use cm^-1 on X-axis instead of 1/ps for spectra.
``-[no]mol``  (no)
    Calculate the velocity acf of 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/>.