.. _gmx vanhove:

gmx vanhove
===========

Synopsis
--------

.. parsed-literal::

    gmx vanhove [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`]
                [:strong:`-om` :emphasis:`[<.xpm>]`] [:strong:`-or` :emphasis:`[<.xvg>]`] [:strong:`-ot` :emphasis:`[<.xvg>]`] [:strong:`-b` :emphasis:`<time>`]
                [:strong:`-e` :emphasis:`<time>`] [:strong:`-dt` :emphasis:`<time>`] [:strong:`-[no]w`] [:strong:`-xvg` :emphasis:`<enum>`]
                [:strong:`-sqrt` :emphasis:`<real>`] [:strong:`-fm` :emphasis:`<int>`] [:strong:`-rmax` :emphasis:`<real>`] [:strong:`-rbin` :emphasis:`<real>`]
                [:strong:`-mmax` :emphasis:`<real>`] [:strong:`-nlevels` :emphasis:`<int>`] [:strong:`-nr` :emphasis:`<int>`] [:strong:`-fr` :emphasis:`<int>`]
                [:strong:`-rt` :emphasis:`<real>`] [:strong:`-ft` :emphasis:`<int>`]

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

``gmx vanhove`` computes the Van Hove correlation function.
The Van Hove G(r,t) is the probability that a particle that is at r_0
at time zero can be found at position r_0+r at time t.
``gmx vanhove`` determines G not for a vector r, but for the length of r.
Thus it gives the probability that a particle moves a distance of r
in time t.
Jumps across the periodic boundaries are removed.
Corrections are made for scaling due to isotropic
or anisotropic pressure coupling.

With option ``-om`` the whole matrix can be written as a function
of t and r or as a function of sqrt(t) and r (option ``-sqrt``).

With option ``-or`` the Van Hove function is plotted for one
or more values of t. Option ``-nr`` sets the number of times,
option ``-fr`` the number spacing between the times.
The binwidth is set with option ``-rbin``. The number of bins
is determined automatically.

With option ``-ot`` the integral up to a certain distance
(option ``-rt``) is plotted as a function of time.

For all frames that are read the coordinates of the selected particles
are stored in memory. Therefore the program may use a lot of memory.
For options ``-om`` and ``-ot`` the program may be slow.
This is because the calculation scales as the number of frames times
``-fm`` or ``-ft``.
Note that with the ``-dt`` option the memory usage and calculation
time can be reduced.

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/.gro/...>] (topol.tpr)
    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:

``-om`` [<.xpm>] (vanhove.xpm) (Optional)
    X PixMap compatible matrix file
``-or`` [<.xvg>] (vanhove_r.xvg) (Optional)
    xvgr/xmgr file
``-ot`` [<.xvg>] (vanhove_t.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
``-sqrt`` <real> (0)
    Use sqrt(t) on the matrix axis which binspacing # in sqrt(ps)
``-fm`` <int> (0)
    Number of frames in the matrix, 0 is plot all
``-rmax`` <real> (2)
    Maximum r in the matrix (nm)
``-rbin`` <real> (0.01)
    Binwidth in the matrix and for ``-or`` (nm)
``-mmax`` <real> (0)
    Maximum density in the matrix, 0 is calculate (1/nm)
``-nlevels`` <int> (81)
    Number of levels in the matrix
``-nr`` <int> (1)
    Number of curves for the ``-or`` output
``-fr`` <int> (0)
    Frame spacing for the ``-or`` output
``-rt`` <real> (0)
    Integration limit for the ``-ot`` output (nm)
``-ft`` <int> (0)
    Number of frames in the ``-ot`` output, 0 is plot all

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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