Tutorials
=========

The tutorials for **ioNERDSS** are provided as Jupyter notebooks, demonstrating how to:

- Set up models for NERDSS  
- Read and process simulation outputs  
- Generate plots and analyses  

Notebook Index
--------------

For detailed description of NERDSS inputs and outputs, please refer to the `NERDSS User Guide <nerdss_user_guide_input_output.html>`_.

Below is a quick reference for the available Jupyter notebooks to prepare the input files and analyze the output files of NERDSS simulations:

.. toctree::
   :maxdepth: 1
   :caption: Jupyter Notebooks

   quick_start
   pdb_to_nerdss_tutorial
   model_setup_for_platonic_solid
   read_pdb_tutorial
   ioNERDSSTutorialSingle
   ioNERDSSTutorialMulti
   GUITutorial
   ClathrinTutorial
   ioNERDSSTutorialGagSphere
   

Additional Resources
--------------------

- For function-by-function details, see the :doc:`api_reference`.
- For installation instructions, see the :doc:`installation`.