Enhanced Sampling Methods for Molecular Dynamics: Algorithms, Implementations, and Applications covers sampling techniques for molecular dynamics studies of equilibrium and kinetics, discussing the theory, algorithm, and implementation of techniques for equilibrium studies, such as Umbrella Sampling, Replica Exchange, Generalized Ensembles, and Metadynamics. The book considers exact and approximate approaches of enhanced sampling, their speed, rate of convergence, and accuracy. Chapters consider path integral formulation, Weighted Ensemble, Transition Path Sampling, and Milestoning.

Finally, simple, detailed examples illustrate enhancements and prepare the reader for their use in more complex systems, making this an ideal resource for computational chemists, biochemists (graduate students and postdoctoral fellows), and computational and theoretical scientists who study molecular processes.

• Outlines the rigorous formulation and comparison of different algorithms
• Provides simple, practical “toy” models for practice to help readers understand how to use them for MD
• Includes an analysis of “real-life," complex applications to demonstrate the capabilities of enhanced sampling approaches
• Helps readers answer critical questions in their own work: what are the bottlenecks involved in simulating a system, what enhanced simulation methods would fit my specific system, what observables are computable, and how to do I analyze the results effectively?