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Examples
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Müller Brown potential
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The transition manifold method is used to compute the reaction coordinates of a two-dimensional synthetic toy system. Working through this example is recommended to everyone trying to understand the basic theory behind the method.

.. toctree::
   :maxdepth: 1

   example_muellerbrown


Alanine dipeptide
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This example demonstrates the analysis of real-world, externally-generated molecular trajectory data. This demonstration is recommended for practitioners aiming at applying the transition manifold method to real-world systems, and requires the understanding of the basic concepts (for example by working through the Müller Brown example).

.. toctree::
   :maxdepth: 1

   example_alaninedipeptide