Replica exchange statistical temperature Monte Carlo

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

doi:10.1063/1.3095422

Cited by 26 publications

(18 citation statements)

References 62 publications

(81 reference statements)

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“…4–29) that approximate the dynamics of a system by considering a reduced set of effective degrees of freedom, at least in part of the system, or part of the simulation time. Other methods to speed up simulations include taking adaptive and/or larger simulation steps,30–32 using different forms of “accelerated” molecular dynamics,33–36 replica exchange/parallel tempering,37–40 implicit solvent models,41 and large‐scale distributed computing 42…”

Section: Introductionmentioning

confidence: 99%

Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides

2009

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The automatic classification of the wealth of molecular configurations gathered in simulation in the form of a few coordinates that help explain the main states and transitions of the system is a recurring problem in computational molecular biophysics. We use the recently proposed ScIMAP algorithm to automatically extract motion parameters from simulation data. The procedure uses only molecular shape similarity and topology information inferred directly from the simulated conformations, and is not biased by a priori known information. The automatically-recovered coordinates prove as excellent reaction coordinates for the molecules studied and can be used to identify stable states and transitions, and as a basis to build free-energy surfaces. The coordinates provide a better description of the free energy landscape when compared with coordinates computed using Principal Components Analysis (PCA), the most popular linear dimensionality reduction technique. The method is first validated on the analysis of the dynamics of an all-atom model of alanine dipeptide, where it successfully recover all previously-known metastable states. When applied to characterize the simulated folding of a coarse-grained model of β-hairpin, in addition to the folded and unfolded states, two symmetric misfolding crossings of the hairpin strands are observed, together with the most likely transitions from one to the other.

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Section: Introductionmentioning

confidence: 99%

Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides

2009

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“…The ability to incorporate specialized MC moves into the WL method can be used to mitigate such problems, increasing sampling and avoid trapping (e.g., cluster moves and identity swaps). The REWL method is also less prone to such trapping issues at low temperatures as a result of the parallel sampling associated with the replica exchange MC moves; prior work has shown this approach to be superior over the original WL method without such exchanges 17 and has additionally been demonstrated for statistical temperature MC 46 (note, statistical temperature MC is closely related to STMD). We note that the replica-exchange technique has been implemented for MD-based computations, specifically in the context of the STMD method, demonstrating increased performance as compared to a single-replica STMD.…”

Section: Discussionmentioning

confidence: 99%

Examining the phase transition behavior of amphiphilic lipids in solution using statistical temperature molecular dynamics and replica-exchange Wang-Landau methods

Gai

Vogel

Maerzke

et al. 2013

The Journal of Chemical Physics

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Two different techniques -replica-exchange Wang-Landau (REWL) and statistical temperature molecular dynamics (STMD) -were applied to systematically study the phase transition behavior of self-assembling lipids as a function of temperature using an off-lattice lipid model. Both methods allow the direct calculation of the density of states with improved efficiency compared to the original Wang-Landau method. A 3-segment model of amphiphilic lipids solvated in water has been studied with varied particle interaction energies (ε) and lipid concentrations. The phase behavior of the lipid molecules with respect to bilayer formation has been characterized through the calculation of the heat capacity as a function of temperature, in addition to various order parameters and general visual inspection. The simulations conducted by both methods can go to very low temperatures with the whole system exhibiting well-ordered structures. With optimized parameters, several bilayer phases are observed within the temperature range studied, including gel phase bilayers with frozen water, mixed water (i.e., frozen and liquid water), and liquid water, and a more fluid bilayer with liquid water. The results obtained from both methods, STMD and REWL, are consistently in excellent agreement with each other, thereby validating both the methods and the results. © 2013 AIP Publishing LLC.

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“…[ ]), and the multicanonical algorithm (MUCA) . Closely related to the MUCA are the Wang–Landau method, statistical temperature methods, and metadynamics . The ST method considers the temperature as a dynamical variable in addition to the (microscopic) state of the system.…”

Section: Introductionmentioning

confidence: 99%

On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics

et al. 2016

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Simulated tempering (ST) is a generalized-ensemble algorithm that employs trajectories exploring a range of temperatures to effectively sample rugged energy landscapes. When implemented using the molecular dynamics method, ST can require the use of short time steps for ensuring the stability of trajectories at high temperatures. To address this shortcoming, a mass-scaling ST (MSST) method is presented in which the particle mass is scaled in proportion to the temperature. Mass scaling in the MSST method leads to velocity distributions that are independent of temperature and eliminates the need for velocity scaling after the accepted temperature updates that are required in conventional ST simulations. The homogeneity in time scales with changing temperature improves the stability of simulations and allows for the use of longer time steps at high temperatures. As a result, the MSST is found to be more efficient than the standard ST method, particularly for cases in which a large temperature range is employed. © 2016 Wiley Periodicals, Inc.

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Replica exchange statistical temperature Monte Carlo

Cited by 26 publications

References 62 publications

Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides

Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides

Examining the phase transition behavior of amphiphilic lipids in solution using statistical temperature molecular dynamics and replica-exchange Wang-Landau methods

On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics

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