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Welcome to CSU-wiki's Documentation!
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Thanks for visiting the CSU Theory Suite's wiki page! 
Feel free to also visit the `Paton Lab Website <https://patonlab.com/>`_ or the `Kim Lab Website <https://bioenergy-kimlab.org/>`_!

.. toctree::
   :maxdepth: 2
   :caption: Adding Packages

   adding_pages/how_to_add_pages.rst


.. toctree::
   :maxdepth: 2
   :caption: Getting Started

   computing_resources/paton_computing_resources.rst
   computing_resources/kim_computing_resources.rst
   computing_resources/essential_unix_commands.rst
   computing_resources/file_system_layout.rst
   computing_resources/running_commands.rst 
   computing_resources/fun_with_coworkers.rst 
   computing_resources/coding_resources.rst
   computing_resources/working_with_files.rst
   computing_resources/moving_renaming_files.rst
   computing_resources/terminal_basics.rst
   computing_resources/working_with_computers.rst
   computing_resources/using_github.rst


.. toctree::
   :maxdepth: 3
   :caption: Helpful Packages

   helpful_packages/helpful_packages.rst


.. toctree::
   :maxdepth: 3
   :caption: Graphical Software

   graphical_software/edition_generation/inkscape_gimp.rst
   graphical_software/edition_generation/matplotlib.rst 
   graphical_software/edition_generation/pymol.rst 


.. toctree::
   :maxdepth: 4
   :caption: Example Workflows

   running_calculations/example_aqme_workflow/example_aqme_workflow.rst
   running_calculations/example_goodvibes_workflow/example_goodvibes_workflow.rst
   running_calculations/example_reggae_workflow/example_reggae_workflow.rst
   running_calculations/example_descriptors_workflow/example_descriptors_workflow.rst
   running_calculations/example_censo_workflow/example_censo_workflow.rst
   running_calculations/example_nciplot_calculation/example_nciplot_calculation.rst
   running_calculations/example_qcalibrate_ts_conf_search/example_qcalibrate_ts_conf_search.rst
   running_calculations/example_yadda_workflow/example_yadda_workflow.rst

.. toctree::
   :maxdepth: 2
   :caption: Concepts

   concepts/classical_molecular_dynamics/classical_molecular_dynamics.rst