Enhanced sampling in AMBER

Sampling Configuration Space

Adaptive Steered Molecular Dynamics
This tutorial provides detailed instructions on how to perform Adaptive Steered Molecular Dynamics (ASMD) simulations. Compared to Steered Molecular Dynamics, ASMD has been shown to converge much faster while reducing the computational cost. The tutorial calculates the Potential Mean Force of unfolding a small alpha-helical peptide using two different velocities. By T. Dwight McGee Jr., Hailey Bureau, Caley Allen, and Rigoberto Hernandez.

The unified “middle” thermostat scheme in AMBER for efficient configurational sampling (Advanced)
This tutorial introduces the "middle" thermostat scheme, which is a unified framework for the development of efficient thermostatting algorityms for configurational sampling for the canonical ensemble. By the Jian Liu research group.

Weighted Ensemble Methods using WESTPA
The WESTPA strategy focuses computing power on transitions rather than stable states. These simulation are more efficient than standard simulations in sampling rare events such as protein binding. By Jeremy Leung and Darian Yang.