.. _gmx mindist:

gmx mindist
===========

Synopsis
--------

.. parsed-literal::

    gmx mindist [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`]
                [:strong:`-od` :emphasis:`[<.xvg>]`] [:strong:`-on` :emphasis:`[<.xvg>]`] [:strong:`-o` :emphasis:`[<.out>]`]
                [:strong:`-ox` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-or` :emphasis:`[<.xvg>]`] [:strong:`-b` :emphasis:`<time>`]
                [:strong:`-e` :emphasis:`<time>`] [:strong:`-dt` :emphasis:`<time>`] [:strong:`-tu` :emphasis:`<enum>`] [:strong:`-[no]w`]
                [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-[no]matrix`] [:strong:`-[no]max`] [:strong:`-d` :emphasis:`<real>`]
                [:strong:`-[no]group`] [:strong:`-[no]pi`] [:strong:`-[no]split`] [:strong:`-ng` :emphasis:`<int>`]
                [:strong:`-[no]pbc`] [:strong:`-[no]respertime`] [:strong:`-[no]printresname`]

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

``gmx mindist`` computes the distance between one group and a number of
other groups. Both the minimum distance
(between any pair of atoms from the respective groups)
and the number of contacts within a given
distance are written to two separate output files.
With the ``-group`` option a contact of an atom in another group
with multiple atoms in the first group is counted as one contact
instead of as multiple contacts.
With ``-or``, minimum distances to each residue in the first
group are determined and plotted as a function of residue number.

With option ``-pi`` the minimum distance of a group to its
periodic image is plotted. This is useful for checking if a protein
has seen its periodic image during a simulation. Only one shift in
each direction is considered, giving a total of 26 shifts. Note
that periodicity information is required from the file supplied with
with ``-s``, either as a .tpr file or a .pdb file with CRYST1 fields.
It also plots the maximum distance within the group and the lengths
of the three box vectors.

Also :doc:`gmx distance <gmx-distance>` and :doc:`gmx pairdist <gmx-pairdist>` calculate distances.

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) (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:

``-od`` [<.xvg>] (mindist.xvg)
    xvgr/xmgr file
``-on`` [<.xvg>] (numcont.xvg) (Optional)
    xvgr/xmgr file
``-o`` [<.out>] (atm-pair.out) (Optional)
    Generic output file
``-ox`` [<.xtc/.trr/...>] (mindist.xtc) (Optional)
    Trajectory: :ref:`xtc` :ref:`trr` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`tng`
``-or`` [<.xvg>] (mindistres.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)
``-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]matrix``  (no)
    Calculate half a matrix of group-group distances
``-[no]max``  (no)
    Calculate *maximum* distance instead of minimum
``-d`` <real> (0.6)
    Distance for contacts
``-[no]group``  (no)
    Count contacts with multiple atoms in the first group as one
``-[no]pi``  (no)
    Calculate minimum distance with periodic images
``-[no]split``  (no)
    Split graph where time is zero
``-ng`` <int> (1)
    Number of secondary groups to compute distance to a central group
``-[no]pbc``  (yes)
    Take periodic boundary conditions into account
``-[no]respertime``  (no)
    When writing per-residue distances, write distance for each time point
``-[no]printresname``  (no)
    Write residue names

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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