title: Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin.
abstract: The capabilities of molecular simulations have been greatly extended by a number of widely used enhanced sampling methods that facilitate escaping from metastable states and crossing large barriers. Despite these developments there are still many problems which remain out of reach for these methods which has led to a vigorous effort in this area. One of the most important problems that remains unsolved is sampling high-dimensional free-energy landscapes and systems that are not easily described by a small number of collective variables. In this work we demonstrate a new way to compute free-energy landscapes of high dimensionality based on the previously introduced variationally enhanced sampling, and we apply it to the miniprotein chignolin.
authors.affiliation: Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zurich and Facoltà di Informatica, Instituto di Scienze Computazionali, Università della Svizzera Italiana, CH-6900 Lugano, Switzerland;
authors.forename: Patrick
authors.initials: P
authors.lastname: Shaffer
authors.affiliation: Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zurich and Facoltà di Informatica, Instituto di Scienze Computazionali, Università della Svizzera Italiana, CH-6900 Lugano, Switzerland; National Center for Computational Design and Discovery of Novel Materials MARVEL, Università della Svizzera Italiana, CH-6900 Lugano, Switzerland.
authors.forename: Omar
authors.initials: O
authors.lastname: Valsson
authors.affiliation: Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zurich and Facoltà di Informatica, Instituto di Scienze Computazionali, Università della Svizzera Italiana, CH-6900 Lugano, Switzerland; National Center for Computational Design and Discovery of Novel Materials MARVEL, Università della Svizzera Italiana, CH-6900 Lugano, Switzerland parrinello@phys.chem.ethz.ch.
authors.forename: Michele
authors.initials: M
authors.lastname: Parrinello
mesh_terms: D000465:Algorithms; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry*; D017510:Protein Folding
chemical_list: D009842:Oligopeptides; C506175:chignolin
keywords: biomolecular simulation; enhanced sampling; free-energy calculation; protein folding