Enhanced sampling methods for molecular dynamics simulations

J Hénin, T Lelièvre, MR Shirts, O Valsson… - arxiv preprint arxiv …, 2022 - arxiv.org
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of
molecular dynamics simulations and allow the sampling of larger portions of the …

Metadynamics

A Barducci, M Bonomi… - Wiley Interdisciplinary …, 2011 - Wiley Online Library
Metadynamics is a powerful technique for enhancing sampling in molecular dynamics
simulations and reconstructing the free‐energy surface as a function of few selected …

Hyperactive learning for data-driven interatomic potentials

C van der Oord, M Sachs, DP Kovács… - npj Computational …, 2023 - nature.com
Data-driven interatomic potentials have emerged as a powerful tool for approximating ab
initio potential energy surfaces. The most time-consuming step in creating these interatomic …

Rethinking metadynamics: from bias potentials to probability distributions

M Invernizzi, M Parrinello - The journal of physical chemistry …, 2020 - ACS Publications
Metadynamics is an enhanced sampling method of great popularity, based on the on-the-fly
construction of a bias potential that is a function of a selected number of collective variables …

The adaptive biasing force method: Everything you always wanted to know but were afraid to ask

J Comer, JC Gumbart, J Hénin, T Lelièvre… - The Journal of …, 2015 - ACS Publications
In the host of numerical schemes devised to calculate free energy differences by way of
geometric transformations, the adaptive biasing force algorithm has emerged as a promising …

Free energy methods for the description of molecular processes

C Chipot - Annual Review of Biophysics, 2023 - annualreviews.org
Efforts to combine theory and experiment to advance our knowledge of molecular processes
relevant to biophysics have been considerably enhanced by the contribution of statistical …

Well-tempered metadynamics: a smoothly converging and tunable free-energy method

A Barducci, G Bussi, M Parrinello - Physical review letters, 2008 - APS
We present a method for determining the free-energy dependence on a selected number of
collective variables using an adaptive bias. The formalism provides a unified description …

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

M Bonomi, D Branduardi, G Bussi, C Camilloni… - Computer Physics …, 2009 - Elsevier
Here we present a program aimed at free-energy calculations in molecular systems. It
consists of a series of routines that can be interfaced with the most popular classical …

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

A Laio, FL Gervasio - Reports on Progress in Physics, 2008 - iopscience.iop.org
Metadynamics is a powerful algorithm that can be used both for reconstructing the free
energy and for accelerating rare events in systems described by complex Hamiltonians, at …

Exploration vs convergence speed in adaptive-bias enhanced sampling

M Invernizzi, M Parrinello - Journal of Chemical Theory and …, 2022 - ACS Publications
In adaptive-bias enhanced sampling methods, a bias potential is added to the system to
drive transitions between metastable states. The bias potential is a function of a few …