.. _gmxapi:

=====================
gmxapi Python package
=====================

Version |gmxapi-version|.

:py:mod:`gmxapi` allows molecular simulation and analysis work to
be staged and run from Python.

After installing |Gromacs| and the gmxapi Python package,
you can use :command:`pydoc gmxapi` from the command line or
``import gmxapi; help(gmxapi)`` within a Python interpreter
for concise usage help.
Complete documentation is collected in the following sections.

.. toctree::
    :maxdepth: 2

    userguide/install
    userguide/usage
    userguide/pythonreference

To discuss *gmxapi*, use the ``#gmxapi`` `tag <https://gromacs.bioexcel.eu/tag/gmxapi>`__
on the |Gromacs| `user discussion forum`_.
Report bugs through the |Gromacs| `issue tracker`_.

Complete documentation for the *gmxapi* Python package
is part of the |Gromacs| `manual <http://manual.gromacs.org/current/>`_
since *gmxapi* version 0.1.
Older releases can also be found at `GitHub <https://www.github.com/kassonlab/gmxapi>`_.
Pre-release documentation may be found at https://manual.gromacs.org/nightly/gmxapi/.

.. seealso::

    gmxapi publications

    Irrgang, M. E., Davis, C., & Kasson, P. M.
    gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support.
    *PLOS Comput Biol* 2022.
    DOI: `10.1371/journal.pcbi.1009835 <https://dx.plos.org/10.1371/journal.pcbi.1009835>`_

    Irrgang, M. E., Hays, J. M., & Kasson, P. M.
    gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations.
    *Bioinformatics* 2018.
    DOI: `10.1093/bioinformatics/bty484 <https://doi.org/10.1093/bioinformatics/bty484>`_