Thompson Group Reference Documentation
=========================================

About this manual and other important links
--------------------------------------------

This documentation covers a variety of topics, including (but not limited to):
**Getting access to the KU Community Cluster**, **PyMOL**, **PACKMOL**, and more. Please see the :ref:`Contents <Contents>` section below for all available tutorials on the site. Other important :ref:`links <links>` are shown below. 

.. _Contents:

Contents
--------

.. toctree::

   Joining the KU Community Cluster
   Basic Terminal Commands
   Cluster Commands
   PyMOL
   VMD (Visual Molecular Dynamics)
   PACKMOL
   MOLDEN
   Developing Molecules for LAMMPS
   Monthly Status Report (MSR)
   Other Resources
   

.. _links:

Other Important Links
----------------------

.. _https://thompsongroup.ku.edu: https://thompsongroup.ku.edu
.. _https://docs.lammps.org/: https://docs.lammps.org/
.. _https://help.ittc.ku.edu/clusterdocs/: https://help.ittc.ku.edu/clusterdocs/
.. _https://www.acs.org: https://www.acs.org

* Thompson Group Website: `https://thompsongroup.ku.edu`_
* LAMMPS Documentation: `https://docs.lammps.org/`_
* KU Cluster Wiki: `https://help.ittc.ku.edu/clusterdocs/`_
* American Chemical Society Website: `https://www.acs.org`_

.. note::

   This project is under active development.

.. toctree::
   :maxdepth: 2
   :caption: Contents: