Adaptively Biased Molecular Dynamics for Free Energy Calculations

TL;DR

The paper introduces an adaptive biased molecular dynamics method for efficient free energy surface computation, featuring low control parameters and scalable extensions, demonstrated on peptide folding simulations.

Contribution

It presents a novel ABMD method inspired by metadynamics with unique features like minimal control parameters and scalable extensions for free energy calculations.

Findings

Efficient free energy surface computation with ABMD.

Successful peptide folding simulation demonstrating method effectiveness.

Scalable extensions improve speed and accuracy.

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.