Examples

Müller Brown potential

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.

• Reaction coordinate analysis of the Müller Brown potential

Alanine dipeptide

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).

• Reaction coordinates of the Alanine dipeptide