Replica exchange with nonequilibrium switches: Enhancing equilibrium sampling by increasing replica overlap

Ballard, Andrew J.; Jarzynski, Christopher

doi:10.1063/1.4712028

Cited by 17 publications

(22 citation statements)

References 38 publications

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“…It is worth noting that fast switching ideas have not only been applied to the calculation of free energies, but have also been combined with existing sampling methods to enhance the efficiency of the simulation. For instance, non-equilibrium switches have been used to improve the acceptance probability of replica exchange simulations [79,80] and to generate trial configurations for Monte Carlo simulations [81,82]. Conversely, waste-recycling Monte Carlo [37] can be adapted for the calculation of free energies from non-equilibrium switching simulations [36].…”

Section: Discussionmentioning

confidence: 99%

Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics

Dellago

Hummer

2013

Entropy

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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.

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Section: Discussionmentioning

confidence: 99%

Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics

Dellago

Hummer

2013

Entropy

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“…In addition, a number of simulation protocols based on nonequilibrium sampling 15-18 have also been recently proposed as well as hybrid algorithms. 19,20 …”

Section: Introductionmentioning

confidence: 99%

A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

Radak

Pabis

et al. 2012

J. Chem. Theory Comput.

150

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A novel variational method for construction of free energy profiles from molecular simulation data is presented. The variational free energy profile (VFEP) method uses the maximum likelihood principle applied to the global free energy profile based on the entire set of simulation data (e.g from multiple biased simulations) that spans the free energy surface. The new method addresses common obstacles in two major problems usually observed in traditional methods for estimating free energy surfaces: the need for overlap in the re-weighting procedure and the problem of data representation. Test cases demonstrate that VFEP outperforms other methods in terms of the amount and sparsity of the data needed to construct the overall free energy profiles. For typical chemical reactions, only ~5 windows and ~20-35 independent data points per window are sufficient to obtain an overall qualitatively correct free energy profile with sampling errors an order of magnitude smaller than the free energy barrier. The proposed approach thus provides a feasible mechanism to quickly construct the global free energy profile and identify free energy barriers and basins in free energy simulations via a robust, variational procedure that determines an analytic representation of the free energy profile without the requirement of numerically unstable histograms or binning procedures. It can serve as a new framework for biased simulations and is suitable to be used together with other methods to tackle with the free energy estimation problem.

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“…In addition, a number of simulation protocols based on non-equilibrium sampling 16–19 have also been recently proposed as well as hybrid algorithms. 20,21 …”

Section: Introductionmentioning

confidence: 99%

Roadmaps through Free Energy Landscapes Calculated Using the Multidimensional vFEP Approach

Radak

Huang

et al. 2013

J. Chem. Theory Comput.

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The variational free energy profile (vFEP) method is extended to two dimensions and tested with molecular simulation applications. The proposed 2D-vFEP approach effectively addresses the two major obstacles to constructing free energy profiles from simulation data using traditional methods: the need for overlap in the re-weighting procedure and the problem of data representation. This is especially evident as these problems are shown to be more severe in two dimensions. The vFEP method is demonstrated to be highly robust and able to provide stable, analytic free energy profiles with only a paucity of sampled data. The analytic profiles can be analyzed with conventional search methods to easily identify stationary points (e.g. minima and first-order saddle points) as well as the pathways that connect these points. These “roadmaps” through the free energy surface are useful not only as a post-processing tool to characterize mechanisms, but can also serve as a basis from which to direct more focused “on-the-fly” sampling or adaptive force biasing. Test cases demonstrate that 2D-vFEP outperforms other methods in terms of the amount and sparsity of the data needed to construct stable, converged analytic free energy profiles. In a classic test case, the two dimensional free energy profile of the backbone torsion angles of alanine dipeptide, 2D-vFEP needs less than 1% of the original data set to reach a sampling accuracy of 0.5 kcal/mol in free energy shifts between windows. A new software tool for performing one and two dimensional vFEP calculations is herein described and made publicly available.

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Replica exchange with nonequilibrium switches: Enhancing equilibrium sampling by increasing replica overlap

Cited by 17 publications

References 38 publications

Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics

Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics

A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

Roadmaps through Free Energy Landscapes Calculated Using the Multidimensional vFEP Approach

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