Generalized Replica Exchange Method

Kim, Jaegil; Keyes, T.; Straub, John E.

doi:10.1063/1.3432176

Cited by 90 publications

(114 citation statements)

References 67 publications

(81 reference statements)

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“…Weight w was set to a small value: 0.006 kcal/mol Å 2 . The restraints were applied to 14 residue pairs: 1 Lys- 17 Cys, 1 Lys- 18 His, 2 Arg- 17 Cys, 2 Arg- 18 His, 3 Cys- 17 Cys, 4 Ser- 17 Cys, 5 Cys- 13 Cys, 5 Cys- 14 Val, 8 Leu- 14 Val, 10 Asp- 14 Val, 11 Lys- 15 Tyr, 12 Glu- 16 Phe, 13 Cys- 17 Cys, and 14 Val- 18 His. The distances for these pairs are smaller than 7.0 Å in the native structure.…”

Section: A Setting the Systemmentioning

confidence: 99%

“…Recently, generalized ensemble methods have been developed for sampling large-scale motions of polypeptides. [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15] A multicanonical Monte Carlo sampling, was introduced to study a physical system, a two-dimensional Potts model, 16 and was subsequently applied to biological systems. [17][18][19] Nakajima et al extended the multicanonical sampling to molecular dynamics (MD), which solves the equations of motion in a Cartesian coordinate space.…”

Section: Introductionmentioning

confidence: 99%

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A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein–protein interaction with an all-atom model in explicit solvent

Higo

Umezawa²,

Nakamura³

2013

The Journal of Chemical Physics

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We propose a novel generalized ensemble method, a virtual-system coupled multicanonical molecular dynamics (V-McMD), to enhance conformational sampling of biomolecules expressed by an all-atom model in an explicit solvent. In this method, a virtual system, of which physical quantities can be set arbitrarily, is coupled with the biomolecular system, which is the target to be studied. This method was applied to a system of an Endothelin-1 derivative, KR-CSH-ET1, known to form an antisymmetric homodimer at room temperature. V-McMD was performed starting from a configuration in which two KR-CSH-ET1 molecules were mutually distant in an explicit solvent. The lowest freeenergy state (the most thermally stable state) at room temperature coincides with the experimentally determined native complex structure. This state was separated to other non-native minor clusters by a free-energy barrier, although the barrier disappeared with elevated temperature.

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Section: A Setting the Systemmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein–protein interaction with an all-atom model in explicit solvent

Higo

Umezawa²,

Nakamura³

2013

The Journal of Chemical Physics

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“…Previously the gREM has been implemented as a generalized Monte Carlo algorithm [20][21][22][23]. Here we introduce a faster constant pressure molecular dynamics (MD) version, by treating the volume as an additional coordinate [24] and introducing effective potential k B T 0 w α (H), where H = U + p 0 V , p 0 is the pressure, and T 0 is the 'kinetic" temperature.…”

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confidence: 99%

Entropic Description of Gas Hydrate Ice-Liquid Equilibrium via Enhanced Sampling of Coexisting Phases

2015

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“…The liquid can be heated up to the liquid spinodal temperature without losing the connectedness among water molecules while forming a full space-spanning connected network of cavity space arising from density fluctuations. On the other hand, at the vapor spinodal temperature (the minimum temperature to which the metastable vapor phase extends), the water-water network of small liquid clusters (i.e., clusterization) just starts to develop in the vapor.To this end, using the generalized replica exchange method (GREM) [25,26], we have performed umbrella sampling for a number of enthalpy windows, with a thermometer in each window. The average temperature T S , thus measured, as a function of configurational enthalpy H and pressure p in the isobaric-isenthalpic ensemble, is the statistical temperature T S ðH; pÞ≡ ð∂S=∂HÞ −1 p , which is a system's intrinsic property.…”

mentioning

confidence: 99%

“…To this end, using the generalized replica exchange method (GREM) [25,26], we have performed umbrella sampling for a number of enthalpy windows, with a thermometer in each window. The average temperature T S , thus measured, as a function of configurational enthalpy H and pressure p in the isobaric-isenthalpic ensemble, is the statistical temperature T S ðH; pÞ≡ ð∂S=∂HÞ −1 p , which is a system's intrinsic property.…”

mentioning

confidence: 99%

Limit of Metastability for Liquid and Vapor Phases of Water

et al. 2014

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We report the limits of superheating of water and supercooling of vapor from Monte Carlo simulations using microscopic models with configurational enthalpy as the order parameter. The superheating limit is well reproduced. The vapor is predicted to undergo spinodal decomposition at a temperature of T vap sp ¼ 46 AE 10°C (0°C ≪ T vap sp ≪ 100°C) under 1 atm. The water-water network begins to form at the supercooling limit of the vapor. Three-dimensional water-water and cavity-cavity unbroken networks are interwoven at critically superheated liquid water; if either network breaks, the metastable state changes to liquid or vapor. DOI: 10.1103/PhysRevLett.112.157802 PACS numbers: 61.20.Ja, 64.60.Q−, 64.70.F− Water is presumably the most used and the most studied substance among all the chemicals known to mankind. In particular, scientists have been attracted to the diverse structures of water clusters, liquid, and ice resulting from different orientations of hydrogen bonds and the associated phenomena [1][2][3][4][5][6][7][8][9][10][11][12][13][14]. However, the liquid-vapor transition of water has been a subject of less intense investigation [15,16] because of difficulties in both experiment and computation due to the complicated metastable states separating the liquid and vapor phases. Given that everyday life experiences water evaporation and dew drops, it is ironic that these physical or chemical phenomena are not adequately understood. Simply, we are familiar with the generally learned fact that water boils at 100°C or 373 K at 1 atm. However, water can be superheated up to 603 K at 1 atm, and water vapor can be supercooled considerably below the boiling point [17][18][19][20][21] though the limit of supercooling is not known yet. This is due to unfavorable energetics at the formation of the liquid-vapor interface, which allow for the temporary existence of metastable states. According to the classical nucleation theory, the metastable states can be kept stable until stochastic fluctuations create the so-called critical cluster, which then grows spontaneously to make a new phase [22].However, these metastable states cease to exist when the liquid or vapor is brought to its stability limit, or spinodal. In this case, where the mother phase completely loses its thermodynamic stability, the phase transition takes place via spinodal decomposition [23]. It differs from classical nucleation in which the phase transition takes place at localized regions of space. Instead, the phase transition is considered to proceed by merging small embryos of daughter phase distributed uniformly over the space [24]. The lifetime of systems near the stability limit is too short to allow for accurate experimental determination of the spinodal. Hence, predicting the stability limit from a microscopic model of matter is of immense importance, given that there are a plethora of phenomena depending on the metastability throughout biology, meteorology, and industry [22].In this Letter, based on targeted sampling of metastable and unsta...

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Generalized Replica Exchange Method

Cited by 90 publications

References 67 publications

A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein–protein interaction with an all-atom model in explicit solvent

A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein–protein interaction with an all-atom model in explicit solvent

Entropic Description of Gas Hydrate Ice-Liquid Equilibrium via Enhanced Sampling of Coexisting Phases

Limit of Metastability for Liquid and Vapor Phases of Water

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