Free energy methods for biomolecular simulations

In the past few years, several methods targeting the computation of the Landau free energy using non-equilibrium dynamics have become popular. These methods introduce a time-dependent potential to bias the original potential energy. In the long time limit, the biasing force is expected to compensate for the free energy gradient, so that the biasing potential eventually reproduces the free energy surface. In this talk we review these methods as well as extensions that enhance sampling of phase space (such as multiple walkers and replica exchange). In particular, we discuss the Adaptively Biased Molecular Dynamics (ABMD) method that was developed in our group and implemented in the AMBER 10-14 codes. We illustrate its capabilities by applying it to challenging systems that undergo a transition in handedness: polyproline peptides that include transitions between the PPII and PPI forms, transitions between B-DNA and Z-DNA, polyglutamine-polyproline systems (in the context of polyglutamine diseases).

References:
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5. Moradi, Babin, Roland and Sagui, Nucleic Acids Research 41, 33 (2013).