Heating and flooding: A unified approach for rapid generation of free energy surfaces

Ming Chen, Michel A. Cuendet, Mark Tuckerman

Research output: Contribution to journalArticle

Abstract

We propose a general framework for the efficient sampling of conformational equilibria in complex systems and the generation of associated free energy hypersurfaces in terms of a set of collective variables. The method is a strategic synthesis of the adiabatic free energy dynamics approach, previously introduced by us and others, and existing schemes using Gaussian-based adaptive bias potentials to disfavor previously visited regions. In addition, we suggest sampling the thermodynamic force instead of the probability density to reconstruct the free energy hypersurface. All these elements are combined into a robust extended phase-space formalism that can be easily incorporated into existing molecular dynamics packages. The unified scheme is shown to outperform both metadynamics and adiabatic free energy dynamics in generating two-dimensional free energy surfaces for several example cases including the alanine dipeptide in the gas and aqueous phases and the met-enkephalin oligopeptide. In addition, the method can efficiently generate higher dimensional free energy landscapes, which we demonstrate by calculating a four-dimensional surface in the Ramachandran angles of the gas-phase alanine tripeptide.

Original languageEnglish (US)
Article number024102
JournalJournal of Chemical Physics
Volume137
Issue number2
DOIs
StatePublished - Jul 14 2012

Fingerprint

Alanine
Heating
Free energy
Gases
free energy
Methionine Enkephalin
Oligopeptides
heating
Dipeptides
Molecular Dynamics Simulation
Thermodynamics
alanine
sampling
vapor phases
Sampling
complex systems
Molecular dynamics
Large scale systems
molecular dynamics
formalism

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry
  • Medicine(all)

Cite this

Heating and flooding : A unified approach for rapid generation of free energy surfaces. / Chen, Ming; Cuendet, Michel A.; Tuckerman, Mark.

In: Journal of Chemical Physics, Vol. 137, No. 2, 024102, 14.07.2012.

Research output: Contribution to journalArticle

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