2024 Amber Workshop Tutorials
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Welcome to the 2024 Amber Workshop Tutorials!

These tutorials were initially created for the 2024 Amber Workshop held at the San Diego Supercomputer Center (SDSC). They are designed to help you understand and utilize Amber for state-of-the-art free energy and machine learning calculations.

As these tutorials were designed to be used in a specific workshop setting, there may be some assumptions about the environment and tools available. However, they are structured to be self-contained, allowing you to follow along independently on
your own system. Unless otherwise noted, these tutorials require some combination of a slurm-based HPC system, Ambertools, Amber, and Gaussian. 

.. warning::

   These tutorials were created prior to the transition to the new york group tutorials page, and thus some links and references may be out of date. We are working to update these tutorials to be fully compatible with the new site.


.. toctree::
   :maxdepth: 5
   :caption: System  Preparation, Visualization, and Ligand Parameterization

   01_vmd_visualization/tutorial.rst
   02_intoMD/tutorial.rst
   03_nonStandardPars/AceticAcid/tutorial.rst
   03_nonStandardPars/MTR1/tutorial.rst
   03_nonStandardPars/TYK2/tutorial.rst

.. toctree::
   :maxdepth: 4
   :caption: Free Energy Tutorials

   04_qmmmMTR1/tutorial.rst
   05_afeSims/asfe/tutorial.rst
   05_afeSims/rbfe/tutorial.rst

.. toctree::
   :maxdepth: 4
   :caption: Machine Learning Potential Tutorials

   06_mlpBookending_gwTP/MTR1/tutorial.rst
   06_mlpBookending_gwTP/mm2qmmm/tutorial.rst