Shortest bond length
====================

The shortest bond length CV is similar to the normal :doc:`bond length <bond>`, but is chosen as \
the minimum of a set of bonds between atom :math:`i` and a list of atoms with indices \
:math:`j, k, l,...`

.. math::
    d_{\mathrm{min}} = \mathrm{min}\left(  \left| r_{j,k,l,...}-r_{i} \right| \right).

The use of the shortest bond length is invoked by the following block in the `meta-config.json` \
file. `atoms1` is the fixed atom :math:`i` and `atom2` is a list of additional atom indices \
:math:`j,k,l,...` to be compared::

    "collective variables": [
      {
        "type": "shortestbond",
        "name": "shortest bond length between atom i and a set of other atoms",
        "atom1": i,
        "atom2": [j, k, l, ...]
      },
      ...
    ]