Adaptively Biased Molecular Dynamics for Free Energy Calculations

Abstract

We present an Adaptively Biased Molecular Dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using non-equilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling methods with an evolving biasing potential, and is inspired by the metadynamics method. The ABMD method has several useful features, including a small number of control parameters, and an $O(t)$ numerical cost with molecular dynamics time $t$. The ABMD method naturally allows for extensions based on multiple walkers and replica exchange, where different replicas can have different temperatures and/or collective variables. This is beneficial not only in terms of the speed and accuracy of a calculation, but also in terms of the amount of useful information that may be obtained from a given simulation. The workings of the ABMD method are illustrated via a study of the folding of the Ace-GGPGGG-Nme peptide in a gaseous and solvated environment.

Revised version to appear in Journal of Chemical Physics

References in corpus (5)

• Escaping free-energy minima
• An efficient, multiple range random walk algorithm to calculate the density of states
• Multidimensional replica-exchange method for free-energy calculations
• Equilibrium free energies from non-equilibrium metadynamics
• Computation of free energy profiles with parallel adaptive dynamics

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