Comparing different protocols of temperature selection in the parallel tempering method

Fiore, Carlos E.

doi:10.1063/1.3636382

Cited by 15 publications

(23 citation statements)

References 31 publications

(32 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…We compare the FEF with other schemes to select the T r 's. We find that the present is not only superior to more simple recipes (like arithmetic progressions (AP)) but also to more physically oriented selection methods (like the constant entropy (CE) [27,28]). We finally confirm a somehow expected result (but not fully investigated in the literature) that the exact distribution of temperatures in T R becomes less relevant as R increases.…”

Section: Introductionmentioning

confidence: 99%

Determining efficient temperature sets for the simulated tempering method

Valentim

Luz

Fiore

2014

Computer Physics Communications

Self Cite

View full text Add to dashboard Cite

In statistical physics, the efficiency of tempering approaches strongly depends on ingredients such as the number of replicas R, reliable determination of weight factors and the set of used temperatures, TR = {T1, T2, . . . , TR}. For the simulated tempering (SP) in particular -useful due to its generality and conceptual simplicity -the latter aspect (closely related to the actual R) may be a key issue in problems displaying metastability and trapping in certain regions of the phase space. To determine TR's leading to accurate thermodynamics estimates and still trying to minimize the simulation computational time, here it is considered a fixed exchange frequency scheme for the ST. From the temperature of interest T1, successive T 's are chosen so that the exchange frequency between any adjacent pair Tr and Tr+1 has a same value f . By varying the f 's and analyzing the TR's through relatively inexpensive tests (e.g., time decay toward the steady regime), an optimal situation in which the simulations visit much faster and more uniformly the relevant portions of the phase space is determined. As illustrations, the proposal is applied to three lattice models, BEG, Bell-Lavis, and Potts, in the hard case of extreme first-order phase transitions, always giving very good results, even for R = 3. Also, comparisons with other protocols (constant entropy and arithmetic progression) to choose the set TR are undertaken. The fixed exchange frequency method is found to be consistently superior, specially for small R's. Finally, distinct instances where the prescription could be helpful (in second-order transitions and for the parallel tempering approach) are briefly discussed.

show abstract

Section: Introductionmentioning

confidence: 99%

Determining efficient temperature sets for the simulated tempering method

Valentim

Luz

Fiore

2014

Computer Physics Communications

Self Cite

View full text Add to dashboard Cite

show abstract

“…151−153 Various tempering methods have also been recently reviewed and compared. 154,155 Among all of these methods, we only focus on the theory and recent applications of enhanced sampling in the CV-space via temperature acceleration. Particularly, TAMD 17,18 is discussed as a promising method to study rare events in biomolecular systems.…”

Section: Enhanced Sampling Methodsmentioning

confidence: 99%

Collective Variable Approaches for Single Molecule Flexible Fitting and Enhanced Sampling

Vashisth

Skiniotis²,

Brooks³

2014

Chem. Rev.

View full text Add to dashboard Cite

“…Attempts to exchange the replicas occur every n s = 10 4 sweeps, using a scheme that alternates attempts between even replicas and their neighbors, and odd replicas and their neighbors. Although one has several manners to define the temperature set [40], here we determine it using an arithmetic progression β α = β 1 + (α − 1) ∆β. We consider N rep = 7 replicas choosing β 1 = 4.2, and ∆β = 0.4.…”

Section: Fibonacci Sequencesmentioning

confidence: 99%

Microcanonical thermostatistics analysis without histograms: Cumulative distribution and Bayesian approaches

Alves

Morero

Rizzi

2015

Computer Physics Communications

View full text Add to dashboard Cite

Microcanonical thermostatistics analysis has become an important tool to reveal essential aspects of phase transitions in complex systems. An efficient way to estimate the microcanonical inverse temperature β(E) and the microcanonical entropy S (E) is achieved with the statistical temperature weighted histogram analysis method (ST-WHAM). The strength of this method lies on its flexibility, as it can be used to analyse data produced by algorithms with generalised sampling weights. However, for any sampling weight, ST-WHAM requires the calculation of derivatives of energy histograms H(E), which leads to non-trivial and tedious binning tasks for models with continuous energy spectrum such as those for biomolecular and colloidal systems. Here, we discuss two alternative methods that avoid the need for such energy binning to obtain continuous estimates for H(E) in order to evaluate β(E) by using ST-WHAM: (i) a series expansion to estimate probability densities from the empirical cumulative distribution function (CDF), and (ii) a Bayesian approach to model this CDF. Comparison with a simple linear regression method is also carried out. The performance of these approaches is evaluated considering coarse-grained protein models for folding and peptide aggregation.

show abstract

Comparing different protocols of temperature selection in the parallel tempering method

Cited by 15 publications

References 31 publications

Determining efficient temperature sets for the simulated tempering method

Determining efficient temperature sets for the simulated tempering method

Collective Variable Approaches for Single Molecule Flexible Fitting and Enhanced Sampling

Microcanonical thermostatistics analysis without histograms: Cumulative distribution and Bayesian approaches

Contact Info

Product

Resources

About