.. _gmx distance:

gmx distance
============

Synopsis
--------

.. parsed-literal::

    gmx distance [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`]
                 [:strong:`-oav` :emphasis:`[<.xvg>]`] [:strong:`-oall` :emphasis:`[<.xvg>]`] [:strong:`-oxyz` :emphasis:`[<.xvg>]`]
                 [:strong:`-oh` :emphasis:`[<.xvg>]`] [:strong:`-oallstat` :emphasis:`[<.xvg>]`] [:strong:`-b` :emphasis:`<time>`]
                 [:strong:`-e` :emphasis:`<time>`] [:strong:`-dt` :emphasis:`<time>`] [:strong:`-tu` :emphasis:`<enum>`]
                 [:strong:`-fgroup` :emphasis:`<selection>`] [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-[no]rmpbc`]
                 [:strong:`-[no]pbc`] [:strong:`-sf` :emphasis:`<file>`] [:strong:`-selrpos` :emphasis:`<enum>`]
                 [:strong:`-seltype` :emphasis:`<enum>`] [:strong:`-select` :emphasis:`<selection>`] [:strong:`-len` :emphasis:`<real>`]
                 [:strong:`-tol` :emphasis:`<real>`] [:strong:`-binw` :emphasis:`<real>`]

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

``gmx distance`` calculates distances between pairs of positions
as a function of time. Each selection specifies an independent set
of distances to calculate. Each selection should consist of pairs
of positions, and the distances are computed between positions 1-2,
3-4, etc.

``-oav`` writes the average distance as a function of time for
each selection.
``-oall`` writes all the individual distances.
``-oxyz`` does the same, but the x, y, and z components of the
distance are written instead of the norm.
``-oh`` writes a histogram of the distances for each selection.
The location of the histogram is set with ``-len`` and
``-tol``. Bin width is set with ``-binw``.
``-oallstat`` writes out the average and standard deviation for
each individual distance, calculated over the frames.

Note that ``gmx distance`` calculates distances between fixed pairs
(1-2, 3-4, etc.) within a single selection.  To calculate distances
between two selections, including minimum, maximum, and pairwise
distances, use :doc:`gmx pairdist <gmx-pairdist>`.

Options
-------

Options to specify input files:

``-f`` [<.xtc/.trr/...>] (traj.xtc) (Optional)
    Input trajectory or single configuration: :ref:`xtc` :ref:`trr` :ref:`cpt` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`tng`
``-s`` [<.tpr/.gro/...>] (topol.tpr) (Optional)
    Input structure: :ref:`tpr` :ref:`gro` :ref:`g96` :ref:`pdb` brk ent
``-n`` [<.ndx>] (index.ndx) (Optional)
    Extra index groups

Options to specify output files:

``-oav`` [<.xvg>] (distave.xvg) (Optional)
    Average distances as function of time
``-oall`` [<.xvg>] (dist.xvg) (Optional)
    All distances as function of time
``-oxyz`` [<.xvg>] (distxyz.xvg) (Optional)
    Distance components as function of time
``-oh`` [<.xvg>] (disthist.xvg) (Optional)
    Histogram of the distances
``-oallstat`` [<.xvg>] (diststat.xvg) (Optional)
    Statistics for individual distances

Other options:

``-b`` <time> (0)
    First frame (ps) to read from trajectory
``-e`` <time> (0)
    Last frame (ps) to read from trajectory
``-dt`` <time> (0)
    Only use frame if t MOD dt == first time (ps)
``-tu`` <enum> (ps)
    Unit for time values: fs, ps, ns, us, ms, s
``-fgroup`` <selection>
    Atoms stored in the trajectory file (if not set, assume first N atoms)
``-xvg`` <enum> (xmgrace)
    Plot formatting: xmgrace, xmgr, none
``-[no]rmpbc``  (yes)
    Make molecules whole for each frame
``-[no]pbc``  (yes)
    Use periodic boundary conditions for distance calculation
``-sf`` <file>
    Provide selections from files
``-selrpos`` <enum> (atom)
    Selection reference positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
``-seltype`` <enum> (atom)
    Default selection output positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
``-select`` <selection>
    Position pairs to calculate distances for
``-len`` <real> (0.1)
    Mean distance for histogramming
``-tol`` <real> (1)
    Width of full distribution as fraction of ``-len``
``-binw`` <real> (0.001)
    Bin width for histogramming

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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