Simulating Enzyme Reactivity: Computational Methods in Enzyme Catalysis
Chapter 6: Free Energy Calculation Methods and Rare Event Sampling Techniques for Biomolecular Simulations
Published:16 Nov 2016
Special Collection: 2016 ebook collection
Jens Smiatek, Niels Hansen, Johannes Kästner, 2016. "Free Energy Calculation Methods and Rare Event Sampling Techniques for Biomolecular Simulations", Simulating Enzyme Reactivity: Computational Methods in Enzyme Catalysis, Inaki Tunon, Vicent Moliner
Download citation file:
We present an overview of free energy methods and rare event sampling techniques which are commonly used in the context of biomolecular simulations at different length scales. Our intention is to focus on the description of the main principles behind these methods. A large number of methods introduce an artificial biasing energy for the calculation of free energies and the sampling of rare events. In contrast, there also exist several other methods which avoid this concept and purely rely on unbiased simulations. Another important factor to distinguish between the methods is the use of reaction coordinates or order parameters. The introduction of reaction coordinates, which can be regarded as a projection onto a few important variables, reduces the phase space significantly. In this reaction coordinate space, lowest free energy pathways can be identified at the price of losing potentially important degrees of freedom. We discuss advantages as well as limitations and highlight the differences and similarities between the methods.