Improved Wang-Landau sampling through the use of smoothed potential-energy surfaces.
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Summary
A method is presented to improve the speed of convergence of Wang-Landau simulations as used to calculate the density of states of continuous systems, using an analytically solvable harmonic system as well as a Go model of a protein.
- Type
- article
- Published
- 2006-04-21
- Cited by
- 6
- References
- 39
- OpenAlex
- https://openalex.org/W2086931702
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:19857803
Keywords
Convergence (economics), Statistical physics, Landau quantization, Energy (signal processing), Sampling (signal processing)
References
- Metropolis Algorithms in Generalized Ensemble
- Flat histogram methods for quantum systems: algorithms to overcome tunneling problems and calculate the free energy.
- Determining the density of states for classical statistical models: a random walk algorithm to produce a flat histogram.
- MONTE CARLO SIMULATION OF A FIRST-ORDER TRANSITION FOR PROTEIN FOLDING
- Algorithmic aspects of multicanonical simulations
- Monte Carlo simulations in generalized isobaric-isothermal ensembles.
- Possible generalization of Boltzmann-Gibbs statistics
- Introduction To Modern Statistical Mechanics
- On the multiple-minima problem in the conformational analysis of molecules: deformation of the potential energy hypersurface by the diffusion equation method
- Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
- Determination of multicanonical weight based on a stochastic model of sampling dynamics.
- Efficient, multiple-range random walk algorithm to calculate the density of states.
- Configurational temperature density of states simulations of proteins.
- Monte Carlo simulation of proteins through a random walk in energy space
- Replica-exchange method using the generalized effective potential.
- Multicanonical algorithms for first order phase transitions
- Structure and energy landscape of a photoswitchable peptide: A replica exchange molecular dynamics study
- On Monte Carlo and molecular dynamics methods inspired by Tsallis statistics: Methodology, optimization, and application to atomic clusters
- Performance of the diffusion equation method in searches for optimum structures of clusters of Lennard-Jones atoms
- Generalized ensemble simulations for complex systems
Cited by
- The thermodynamics of charged defects in ionic crystals
- Non -Boltzmann sampling for the accurate calculation of peptide-surface adsorption free energy
- Simple and effective application of the Wang-Landau method for multicanonical molecular dynamics simulation.
- Lumping analysis for the prediction of long-time dynamics: from monomolecular reaction systems to inherent structure dynamics of glassy materials.
- Computational applications of nonextensive statistical mechanics
- Some comments on Monte Carlo and molecular dynamics methods
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