.. _tutorials:

Tutorials
=========

Here you can find a list of available tutorials that provide input files and
a step-by-step guide on how to perform alchemical free energy calculations using
**pmx** for a few typical use cases:

.. toctree::
   :maxdepth: 1

   protein_mut
   ligand_mut
   nucleic_mut
   large_scale_scans
   analysis


Before getting straight into the simulations, we would suggest to familiarise
yourself with the concepts at the foundation of this type of calculations as
well as with how **pmx** works. In this regard, here we provide a few useful references:

1. V. Gapsys, S. Michielssens, D. Seeliger, B.L. de Groot; `pmx: Automated protein structure and topology generation for alchemical perturbations <https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.23804>`_; *J. Comp. Chem.* **2014**, 36(5), 348--354
2. V. Gapsys, S. Michielssens, J.H. Peters, B.L. de Groot, H. Leonov; `Calculation of binding free energies <https://link.springer.com/protocol/10.1007/978-1-4939-1465-4_9>`_; *Method Mol. Biol* **2015**, vol. 1215, Humana Press
3. M. Aldeghi, B.L. de Groot, V. Gapsys; `Accurate calculation of free energy changes upon amino acid mutation <https://link.springer.com/>`_; *Method Mol. Biol* **2018**, vol. XXXX, Humana Press