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Entropy 2014, 16(1), 41-61; doi:10.3390/e16010041

Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics

1
Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
2
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
*
Author to whom correspondence should be addressed.
Received: 10 October 2013 / Revised: 12 November 2013 / Accepted: 19 November 2013 / Published: 27 December 2013
(This article belongs to the Special Issue Molecular Dynamics Simulation)
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Abstract

As shown by Jarzynski, free energy differences between equilibrium states can be expressed in terms of the statistics of work carried out on a system during non-equilibrium transformations. This exact result, as well as the related Crooks fluctuation theorem, provide the basis for the computation of free energy differences from fast switching molecular dynamics simulations, in which an external parameter is changed at a finite rate, driving the system away from equilibrium. In this article, we first briefly review the Jarzynski identity and the Crooks fluctuation theorem and then survey various algorithms building on these relations. We pay particular attention to the statistical efficiency of these methods and discuss practical issues arising in their implementation and the analysis of the results.
Keywords: fast switching simulations; non-equilibrium work theorem; fluctuation theorem; non-equilibrium molecular dynamics fast switching simulations; non-equilibrium work theorem; fluctuation theorem; non-equilibrium molecular dynamics
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This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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Dellago, C.; Hummer, G. Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics. Entropy 2014, 16, 41-61.

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