Umbrella sampling

Abstract The calculation of free‐energy differences is one of the main challenges in computational biology and biochemistry. Umbrella sampling, biased molecular dynamics (MD), is one of the methods that provide free energy along a reaction coordinate. Here, the method is derived in a historic overview and is compared with related methods like thermodynamic integration, slow growth, steered MD, or the Jarzynski‐based fast‐growth technique. In umbrella sampling, bias potentials along a (one‐ or more‐dimensional) reaction coordinate drive a system from one thermodynamic state to another (e.g., reactant and product). The intermediate steps are covered by a series of windows, at each of which an MD simulation is…

• DF
  Deutsche Forschungsgemeinschaft