Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
- 18 January 2008
- journal article
- research article
- Published by American Physical Society (APS) in Physical Review Letters
- Vol. 100 (2), 020603
- https://doi.org/10.1103/physrevlett.100.020603
Abstract
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 which has metadynamics and canonical sampling as limiting cases. Convergence and errors can be rigorously and easily controlled. The parameters of the simulation can be tuned so as to focus the computational effort only on the physically relevant regions of the order parameter space. The algorithm is tested on the reconstruction of an alanine dipeptide free-energy landscape.Keywords
This publication has 37 references indexed in Scilit:
- A Bias-Exchange Approach to Protein FoldingThe Journal of Physical Chemistry B, 2007
- From A to B in free energy spaceThe Journal of Chemical Physics, 2007
- Canonical sampling through velocity rescalingThe Journal of Chemical Physics, 2007
- Hsc70 ATPase: An Insight into Water Dissociation and Joint Catalytic Role of K+ and Mg2+ Metal Cations in the Hydrolysis ReactionJournal of the American Chemical Society, 2006
- The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling correctionsThe Journal of Chemical Physics, 2006
- Glycine at the Pyrite−Water Interface: The Role of Surface DefectsJournal of the American Chemical Society, 2006
- Deprotonation of Solvated Formic Acid: Car−Parrinello and Metadynamics SimulationsThe Journal of Physical Chemistry B, 2006
- Mapping potential energy surfacesThe Journal of Chemical Physics, 2004
- All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of ProteinsThe Journal of Physical Chemistry B, 1998
- Stochastic Gradient Approximation: An Efficient Method to Optimize Many-Body Wave FunctionsPhysical Review Letters, 1997