New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles

Lyubartsev, Alexander P.; Martsinovski, A. A.; Шевкунов, С. В.; Vorontsov-Vèlyaminov, P. N.

doi:10.1063/1.462133

Cited by 993 publications

(903 citation statements)

References 21 publications

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“…A number of methods, such as multicanonical ensemble, 22,23 simulated tempering, 24,25 and the replica exchange method (REM), [26][27][28][29] were designed to address this issue. The REM was proposed 26,30 in the context of Ising spin glasses 31 and introduced to proteinlike systems by Sugita and Okamoto.…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics of Apo-Adenylate Kinase: A Distance Replica Exchange Method for the Free Energy of Conformational Fluctuations

2006

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A large domain motion in adenylate kinase from E. coli (AKE) is studied with molecular dynamics. AKE undergoes a large-scale rearrangement of its lid and AMP-binding domains when the open form closes over its substrates, AMP, and Mg 2+ -ATP, whereby the AMP-binding and lid domains come closer to the core. The third domain, the core, is relatively stable during this motion. A reaction coordinate that monitors the distance between the AMP-binding and core domains is selected to be able to compare with the results of energy transfer experiments. Sampling along this reaction coordinate is carried out by using a distance replica exchange method (DREM), where systems that differ by a restraint potential enforcing different reaction coordinate values are independently simulated with periodic attempts at exchange of these systems. Several methods are used to study the efficiency and convergence properties of the DREM simulation and compared with an analogous non-DREM simulation. The DREM greatly accelerates the rate and extent of configurational sampling and leads to equilibrium sampling as measured by monitoring collective modes obtained from a principal coordinate analysis. The potential of mean force along the reaction coordinate reveals a rather flat region for distances from the open to a relatively closed AKE conformation. The potential of mean force for smaller distances has a distinct minimum that is quite close to that found in the closed form X-ray structure. In concert with a decrease in the reaction coordinate distance (AMP-binding-to-core distance) the lid-to-core distance of AKE also decreases. Therefore, apo AKE can fluctuate from its open form to conformations that are quite similar to its closed form X-ray structure, even in the absence of its substrates.

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Section: Introductionmentioning

confidence: 99%

Molecular Dynamics of Apo-Adenylate Kinase: A Distance Replica Exchange Method for the Free Energy of Conformational Fluctuations

2006

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“…In that sense, it differs from the simulated annealing in which the system goes away from the equilibrium state while changing the temperature. As a generalized ensemble technique, simulated tempering algorithm [12,30] simulates the ensemble by partition function;…”

Section: Methodsmentioning

confidence: 99%

Secondary structure prediction of beta-hairpin peptide tryptophan zipper-I

Gökoğlu

Çelik

2008

Physica A: Statistical Mechanics and its Applications

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We have investigated the folding properties of tryptophan zipper-I molecule which folds into a stable β-hairpin motif in aqueous solution as suggested by nuclear magnetic resonance (NMR) experiments. An all-atom presentation, including hydrogen, was used with an implicit solvent. As a simulation technique, simulated tempering algorithm was used to obtain equilibrium conformations of the molecule at ten distinct temperatures. Our minimum energy configuration obtained from simulated tempering algorithm is a β-hairpin motif with 1.30Å backbone root-mean-square deviation from the reference PDB structure (1le0.pdb). Several quantities and exhaustive folding free energy landscapes were determined and discussed in order to clarify the folding behavior.

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“…Another phenomenon was, that at 1991 ± 5 years a number of papers [5,6,11,10,12] emerged in the literature, which all aimed at improving MCMC calculations by extending the confines of the canonical ensemble. Most important has been the replica exchange method, which is also known under the names parallel tempering and multiple Markov chains.…”

Section: Generalized Ensemblesmentioning

confidence: 99%

“…The Gibbs or Boltzmann ensemble E B is defined to be the ensemble with the probability distribution (10).…”

Section: Importance Sampling and Markov Chain Monte Carlomentioning

confidence: 99%

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Markov Chain Monte Carlo Methods for Simulations of Biomolecules

Berg

Lecture Notes in Physics

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The computer revolution has been driven by a sustained increase of computational speed of approximately one order of magnitude (a factor of ten) every five years since about 1950. In natural sciences this has led to a continuous increase of the importance of computer simulations. Major enabling techniques are Markov Chain Monte Carlo (MCMC) and Molecular Dynamics (MD) simulations.This article deals with the MCMC approach. First basic simulation techniques, as well as methods for their statistical analysis are reviewed. Afterwards the focus is on generalized ensembles and biased updating, two advanced techniques, which are of relevance for simulations of biomolecules, or are expected to become relevant with that respect. In particular we consider the multicanonical ensemble and the replica exchange method (also known as parallel tempering or method of multiple Markov chains).

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New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles

Cited by 993 publications

References 21 publications

Molecular Dynamics of Apo-Adenylate Kinase: A Distance Replica Exchange Method for the Free Energy of Conformational Fluctuations

Molecular Dynamics of Apo-Adenylate Kinase: A Distance Replica Exchange Method for the Free Energy of Conformational Fluctuations

Secondary structure prediction of beta-hairpin peptide tryptophan zipper-I

Markov Chain Monte Carlo Methods for Simulations of Biomolecules

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