.. _examples:

Examples
========

Here are some examples on how to use the **pmx** library to carry out the key
steps in the setup and analysis of alchemical free energy calculations. Using
the API is useful if you want to automate the setup for many calculations.


.. toctree::
   :maxdepth: 1

   mutate
   hybrid_topology
   analysis


Another way to setup the files needed for the calculations is via the
:ref:`command line tools<scripts>`, which may be more convenient to use for a
small number of calculations.