Tutorials
=========

Step-by-step guides for common workflows.

.. toctree::
   :maxdepth: 1

   basic_simulation
   ligand_systems
   hpc_deployment
   analysis_workflows

Getting Started
---------------

:doc:`basic_simulation`
   Complete walkthrough of building, running, and analyzing a simple protein 
   simulation. Good starting point for new users.

Advanced Topics
---------------

:doc:`ligand_systems`
   Working with protein-ligand systems including small molecule parameterization 
   with GAFF2.

:doc:`hpc_deployment`
   Deploying simulations on HPC clusters with Parsl, including configuration 
   for PBS schedulers and GPU allocation.

:doc:`analysis_workflows`
   Comprehensive analysis pipelines combining multiple analysis tools for 
   characterizing binding interfaces.