Literature DB >> 16460155

Equilibrium free energies from fast-switching trajectories with large time steps.

Wolfgang Lechner1, Harald Oberhofer, Christoph Dellago, Phillip L Geissler.   

Abstract

Jarzynski's [Phys. Rev. Lett. 78, 2690 (1997)] identity for the free-energy difference between two equilibrium states can be viewed as a special case of a more general procedure based on phase-space mappings. Solving a system's equation of motion by approximate means generates a mapping that is perfectly valid for this purpose, regardless of how closely the solution mimics true time evolution. We exploit this fact, using crudely dynamical trajectories to compute free-energy differences that are in principle exact. Numerical simulations show that Newton's equation can be discretized to low order over very large time steps (limited only by the computer's ability to represent resulting values of dynamical variables) without sacrificing thermodynamic accuracy. For computing the reversible work required to move a particle through a dense liquid, these calculations are more efficient than conventional fast-switching simulations by more than an order of magnitude. We also explore consequences of the phase-space mapping perspective for systems at equilibrium, deriving an exact expression for the statistics of energy fluctuations in simulated conservative systems.

Year:  2006        PMID: 16460155     DOI: 10.1063/1.2162874

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  6 in total

1.  Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation.

Authors:  Jerome P Nilmeier; Gavin E Crooks; David D L Minh; John D Chodera
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-24       Impact factor: 11.205

2.  Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise.

Authors:  Paul Maragakis; Felix Ritort; Carlos Bustamante; Martin Karplus; Gavin E Crooks
Journal:  J Chem Phys       Date:  2008-07-14       Impact factor: 3.488

3.  Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics - Monte Carlo Canonical Propagation Algorithm.

Authors:  Yunjie Chen; Seyit Kale; Jonathan Weare; Aaron R Dinner; Benoît Roux
Journal:  J Chem Theory Comput       Date:  2016-03-25       Impact factor: 6.006

4.  Replica exchange with nonequilibrium switches.

Authors:  Andrew J Ballard; Christopher Jarzynski
Journal:  Proc Natl Acad Sci U S A       Date:  2009-07-10       Impact factor: 11.205

Review 5.  Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding.

Authors:  Hagai Meirovitch; Srinath Cheluvaraja; Ronald P White
Journal:  Curr Protein Pept Sci       Date:  2009-06       Impact factor: 3.272

6.  Entropy, Free Energy, and Work of Restricted Boltzmann Machines.

Authors:  Sangchul Oh; Abdelkader Baggag; Hyunchul Nha
Journal:  Entropy (Basel)       Date:  2020-05-11       Impact factor: 2.524

  6 in total

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