Low-Temperature Structural Transitions: Circumventing the Broken-Ergodicity Problem

Sharapov, V. A.; Meluzzi, Dario; Mandelshtam, Vladimir A.

doi:10.1103/physrevlett.98.105701

Cited by 77 publications

(101 citation statements)

References 19 publications

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“…It is important to emphasize that caution must always be exercised when dealing with sparse distributions. As discussed elsewhere, 22 for example, tempering methods alone may be inadequate for the treatment of systems that exhibit lowtemperature, solid-solid transitions. The CEI method presented here is thus intended as a way to improve the efficiency of tempering approaches in situations where they are appropriate, as opposed to a means for extending their intrinsic applicability.…”

Section: Discussionmentioning

confidence: 99%

A constant entropy increase model for the selection of parallel tempering ensembles

Sabo

Meuwly

Freeman

et al. 2008

The Journal of Chemical Physics

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The present paper explores a simple approach to the question of parallel tempering temperature selection. We argue that to optimize the performance of parallel tempering it is reasonable to require that the increase in entropy between successive temperatures be uniform over the entire ensemble. An estimate of the system's heat capacity, obtained either from experiment, a preliminary simulation, or a suitable physical model, thus provides a means for generating the desired tempering ensemble. Applications to the two-dimensional Ising problem indicate that the resulting method is effective, simple to implement, and robust with respect to its sensitivity to the quality of the underlying heat capacity model.

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Section: Discussionmentioning

confidence: 99%

A constant entropy increase model for the selection of parallel tempering ensembles

Sabo

Meuwly

Freeman

et al. 2008

The Journal of Chemical Physics

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“…10 Due to the double-funneled energy landscape of LJ 31 , associated with the Mackay→ anti-Mackay transition, the heat capacity displays a narrow peak around T Ϸ 0.027 besides a core melting peak around T Ϸ 0.32. This solid-solid transition is very sensitive to the convergence of simulations, 11,12,23,55 which makes LJ 31 a good benchmark for newly developed sampling algorithms in a rugged energy landscape. A recent study 12 reported that a single replica enhanced sampling employing the Wang-Landau 56 or the multicanonical algorithm 29 failed to capture a correct thermodynamics of the solid-solid transition.…”

Section: Applications: Lj 31 Atom Clustersmentioning

confidence: 99%

Optimal replica exchange method combined with Tsallis weight sampling

Kim

Straub²

2009

The Journal of Chemical Physics

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A unified framework integrating the generalized ensemble sampling associated with the Tsallis weight ͓C. Tsallis, J. Stat. Phys. 52, 479 ͑1988͔͒ and the replica exchange method ͑REM͒ has been proposed to accelerate the convergence of the conventional temperature REM ͑t-REM͒. Using the effective temperature formulation of the Tsallis weight sampling, it is shown that the average acceptance probability for configurational swaps between neighboring replicas in the combination of Tsallis weight sampling and REM ͑Tsallis-REM͒ is directly proportional to an overlap integral of the energy distributions of neighboring replicas as in the t-REM. Based on this observation, we suggest a robust method to select optimal Tsallis parameters in the conventional parametrization scheme and present new parametrization schemes for the Tsallis-REM, which significantly improves the acceptance of configurational swaps by systematically modulating energy overlaps between neighboring replicas. The distinguished feature of our method is that all relevant parameters in the Tsallis-REM are automatically determined from the equilibrium phase simulation using the t-REM. The overall performance of our method is explicitly demonstrated for various simulation conditions for the Lennard-Jones 31 atom clusters, exhibiting a double-funneled energy landscape.

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“…This approach to binding free energy calculations is employed in the mining minima algorithm, 35 which has been successfully applied to various biomacromolecular systems, especially small host-guest systems. Benchmark superposition calculations for atomic and molecular clusters show that the energy landscape approach can be much faster than MD or MC based methods, especially for cases of broken ergodicity, 36,37,[37][38][39] since the superposition partition function is explicitly ergodic.…”

Section: Introductionmentioning

confidence: 99%

A conformational factorisation approach for estimating the binding free energies of macromolecules

Mochizuki

Whittleston

Somani

et al. 2014

Phys. Chem. Chem. Phys.

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Publisher's copyright statement:Additional information: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-pro t purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. We present a conformational factorization approach. The theory is based on a superposition partition function, where the partition function is written as a sum over contributions from local minima. The factorisation greatly reduces the number of minima that need to be considered, by employing the same local configurations for groups that are sufficiently distant from the binding site. The theory formalises the conditions required to analyse how our definition of the binding site region affects the free energy difference between the apo and holo states. We employ basin-hopping parallel tempering to sample minima that contribute significantly to the partition function, and calculate the binding free energies within the harmonic normal mode approximation. A further significant gain in efficiency is achieved using a recently developed local rigid body framework in both the sampling and the normal mode analysis, which reduces the number of degrees of freedom. We benchmark this approach for human aldose reductase (PDB code 2INE). When varying the size of the rigid region, the free energy difference converges for factorisation of groups at a distance of 14Å from the binding site, which corresponds to 80% of the protein being locally rigidified. This approach is likely to be useful for estimating the binding free energy of protein-ligand complexes.

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Low-Temperature Structural Transitions: Circumventing the Broken-Ergodicity Problem

Cited by 77 publications

References 19 publications

A constant entropy increase model for the selection of parallel tempering ensembles

A constant entropy increase model for the selection of parallel tempering ensembles

Optimal replica exchange method combined with Tsallis weight sampling

A conformational factorisation approach for estimating the binding free energies of macromolecules

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