Simulated Tempering: A New Monte Carlo Scheme

Marinari, Enzo; Parisi, Giorgio

doi:10.1209/0295-5075/19/6/002

Cited by 1,641 publications

(1,500 citation statements)

References 20 publications

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“…REM [11][12][13][14] consists in performing a series of independent simulations of the same system, each in a different equilibrium condition. In its most common implementation, each replica of the system has a different temperature, going gradually from the temperature of interest T 0 to a higher temperature T M , high enough to enhance barrier-crossing efficiency and sampling of metastable conformers.…”

Section: Replica Exchange Methodsmentioning

confidence: 99%

“…With this choice, the latter interactions do not enter in the acceptance probability of eq. (13). On the other hand, conformational transitions in proteins are mainly driven by torsional and solute-solute and solute-solvent non bonded interactions.…”

Section: Implementation In Oracmentioning

confidence: 99%

“…The Replica Exchange Method (REM) [11][12][13][14] provides an elegant and simple solution to quasiergodic sampling. In REM, several independent trajectories, called replicas, are simultaneously generated in different thermodynamic conditions.…”

Section: Introductionmentioning

confidence: 99%

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ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

et al. 2009

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Abstract:We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834, a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at

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Section: Replica Exchange Methodsmentioning

confidence: 99%

Section: Implementation In Oracmentioning

confidence: 99%

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ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

et al. 2009

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“…The states of the chains are occasionally exchanged, allowing chains with small proposal widths to make large jumps. Simulated tempering (Marinari & Parisi, 1992) is a similar algorithm, but instead of running several chains in parallel, one chain is run and transition kernels of different temperatures are swapped. These ideas provide help in most applications, and it may be possible to apply them in the human MCMC procedure.…”

Section: Cautions and Recommendationsmentioning

confidence: 99%

Uncovering mental representations with Markov chain Monte Carlo

Sanborn

Griffiths

Shiffrin

2010

Cognitive Psychology

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A note on versions:The version presented here may differ from the published version or, version of record, if you wish to cite this item you are advised to consult the publisher's version. Please see the 'permanent WRAP URL' above for details on accessing the published version and note that access may require a subscription. Richard M. Shiffrin Indiana University, Bloomington Abstract A key challenge for cognitive psychology is the investigation of mental representations, such as object categories, subjective probabilities, choice utilities, and memory traces. In many cases, these representations can be expressed as a non-negative function defined over a set of objects. We present a behavioral method for estimating these functions. Our approach uses people as components of a Markov chain Monte Carlo (MCMC) algorithm, a sophisticated sampling method originally developed in statistical physics. Experiments 1 and 2 verified the MCMC method by training participants on various category structures and then recovering those structures. Experiment 3 demonstrated that the MCMC method can be used estimate the structures of the real-world animal shape categories of giraffes, horses, dogs, and cats. Experiment 4 combined the MCMC method with multidimensional scaling to demonstrate how different accounts of the structure of categories, such as prototype and exemplar models, can be tested, producing samples from the categories of apples, oranges, and grapes.

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“…31 In contrast to that method, the SREM does not require synchronization between the different walkers (processors), leaves no CPUs idle, and thus has substantially lower overhead. Another method suitable for distributed environments is simulated tempering, 32 which is inherently a serial algorithm. The primary issue with that method is the determination of the free energy constants, which has historically required a somewhat involved iterative procedure.…”

Section: Discussionmentioning

confidence: 99%

Serial Replica Exchange

et al. 2007

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Parallel tempering (or the replica exchange method (REM)) is a powerful method for speeding up the sampling of conformational states of systems with rough energy landscapes, like proteins, where stable conformational states can be separated by large energy barriers. The usual implementation of the REM is performed on local computer clusters (or parallel processors) where the different replicas must be run synchronously. Here, we present serial replica exchange (SREM), a method that is equivalent to the standard REM in terms of efficiency yet runs asynchronously on a distributed network of computers. A second advantage is the method's greatly enhanced fault tolerance, which enables the study of biological systems on worldwide distributed computing environments, such as Folding@Home. 1 For proof of concept, we apply the SREM to a single alanine dipeptide molecule in explicit water. We show that the SREM reproduces the thermodynamic and structural properties determined by the REM.

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Simulated Tempering: A New Monte Carlo Scheme

Cited by 1,641 publications

References 20 publications

ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

Uncovering mental representations with Markov chain Monte Carlo

Serial Replica Exchange

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