(Q34279694)

1 August 2017

title

Generalized simulated tempering for exploring strong phase transitions (English)

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1 August 2017

Jaegil Kim

1

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1 August 2017

John E Straub

series ordinal

2

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1 August 2017

language of work or name

English

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publication date

1 October 2010

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Journal of Chemical Physics

1 August 2017

published in

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1 August 2017

volume

133

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1 August 2017

issue

15

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1 August 2017

page(s)

154101

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Enhanced sampling and applications in protein folding in explicit solvent

1 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2973984

Generalized replica exchange method

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2973984

Error and efficiency of simulated tempering simulations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2973984

Optimal replica exchange method combined with Tsallis weight sampling

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2973984

Replica exchange statistical temperature Monte Carlo

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2973984

Simulated tempering yields insight into the low-resolution Rosetta scoring functions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2973984

Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2973984

Simulation via direct computation of partition functions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2973984

Statistical temperature molecular dynamics: application to coarse-grained beta-barrel-forming protein models

6 July 2018

1 reference

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Replica exchange with solute tempering: a method for sampling biological systems in explicit water

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2973984

Performance Limitations of Flat-Histogram Methods

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2973984

Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram

6 July 2018

1 reference

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Generalized-ensemble algorithms for molecular simulations of biopolymers

6 July 2018

1 reference

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Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2973984

Negative Heat Capacity for a Cluster of 147 Sodium Atoms

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2973984

Three-helix-bundle protein in a Ramachandran model

6 July 2018

1 reference

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New Monte Carlo algorithm: Entropic sampling.

6 July 2018

1 reference

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Novel methods of sampling phase space in the simulation of biological systems

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2973984

Replica Monte Carlo simulation of spin glasses.

6 July 2018

1 reference

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

Optimized parallel tempering simulations of proteins.

21 January 2018

1 reference

Structure optimization and folding mechanisms of off-lattice protein models using statistical temperature molecular dynamics simulation: Statistical temperature annealing.

21 January 2018

1 reference

Monte Carlo simulations in generalized ensemble: Multicanonical algorithm versus simulated tempering.

21 January 2018

1 reference

Choosing weights for simulated tempering

21 January 2018

1 reference

Simulated Tempering Distributed Replica Sampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methods for Conformational Sampling.

21 January 2018

1 reference

Comparison of the serial and parallel algorithms of generalized ensemble simulations: an analytical approach.

21 January 2018

1 reference

Comparison of sampling efficiency between simulated tempering and replica exchange

21 January 2018

1 reference

From multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering.

21 January 2018

1 reference

Simulated-tempering replica-exchange method for the multidimensional version.

21 January 2018

1 reference

Comparison between integrated and parallel tempering methods in enhanced sampling simulations

21 January 2018

1 reference

Relationship between protein folding thermodynamics and the energy landscape

21 January 2018

1 reference

Dynamical origin of uniform sampling in multicanonical ensemble.

21 January 2018

1 reference

Possible generalization of Boltzmann-Gibbs statistics

21 January 2018

1 reference

Efficient parallel tempering for first-order phase transitions.

21 January 2018

1 reference

Replica-exchange method using the generalized effective potential.

21 January 2018

1 reference

All-atom level direct folding simulation of a betabetaalpha miniprotein.

21 January 2018

1 reference

Performances of Wang-Landau algorithms for continuous systems.

21 January 2018

1 reference

Comment on "The incomplete beta function law for parallel tempering sampling of classical canonical systems" [J. Chem. Phys. 120, 4119 (2004)].

21 January 2018

1 reference

Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics

21 January 2018

1 reference

Optimal allocation of replicas in parallel tempering simulations.

21 January 2018

1 reference

Multidimensional generalized-ensemble algorithms for complex systems.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2973984

Statistical-temperature Monte Carlo and molecular dynamics algorithms.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2973984

Generalized simulated annealing algorithms using Tsallis statistics: Application to conformational optimization of a tetrapeptide.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2973984

Generalized-ensemble Monte Carlo method for systems with rough energy landscape

28 October 2018

1 reference

Replica-exchange simulated tempering method for simulations of frustrated systems

21 January 2018

1 reference

Generalized simulated tempering realized on expanded ensembles of non-Boltzmann weights

21 January 2018

1 reference

12 December 2020

Simulated Solute Tempering

1 reference

12 December 2020

Tsallis dynamics using the Nosé-Hoover approach

1 reference

12 December 2020

Adaptive integration method for Monte Carlo simulations

1 reference

12 December 2020

New Monte Carlo technique for studying phase transitions

1 reference

12 December 2020

Microcanonical versus canonical analysis of protein folding

1 reference

12 December 2020

Gaussian ensemble as an interpolating ensemble

1 reference

12 December 2020

Stochastic formulation of sampling dynamics in generalized ensemble methods

1 reference

12 December 2020

Coexistence in finite systems

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12 December 2020

Microcanonical Analyses of Peptide Aggregation Processes

1 reference

12 December 2020

Simulated-tempering procedure for spin-glass simulations

1 reference

12 December 2020

Optimized Monte Carlo data analysis

1 reference

12 December 2020

Statistical thermodynamics of the cluster solid-liquid transition

1 reference

12 December 2020

New approach to spin-glass simulations

1 reference

12 December 2020

Identifiers

DOI

10.1063/1.3503503

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1 August 2017

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1 August 2017

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