Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing
出版年份 2011 全文链接
标题
Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing
作者
关键词
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出版物
JOURNAL OF CHEMICAL PHYSICS
Volume 135, Issue 19, Pages 194110
出版商
AIP Publishing
发表日期
2011-11-23
DOI
10.1063/1.3660669
参考文献
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- (2012) Dawn Woodard et al. ELECTRONIC JOURNAL OF PROBABILITY
- Measure-preserving integrators for molecular dynamics in the isothermal–isobaric ensemble derived from the Liouville operator
- (2010) Tang-Qing Yu et al. CHEMICAL PHYSICS
- OpenMM: A Hardware-Independent Framework for Molecular Simulations
- (2010) Peter Eastman et al. COMPUTING IN SCIENCE & ENGINEERING
- Generalized Replica Exchange Method
- (2010) Jaegil Kim et al. JOURNAL OF CHEMICAL PHYSICS
- Error and efficiency of simulated tempering simulations
- (2010) Edina Rosta et al. JOURNAL OF CHEMICAL PHYSICS
- Automated Sampling Assessment for Molecular Simulations Using the Effective Sample Size
- (2010) Xin Zhang et al. Journal of Chemical Theory and Computation
- Optimal Weights in Serial Generalized-Ensemble Simulations
- (2010) Riccardo Chelli Journal of Chemical Theory and Computation
- Exchange Often and Properly in Replica Exchange Molecular Dynamics
- (2010) Daniel J. Sindhikara et al. Journal of Chemical Theory and Computation
- Constant pH Replica Exchange Molecular Dynamics in Biomolecules Using a Discrete Protonation Model
- (2010) Yilin Meng et al. Journal of Chemical Theory and Computation
- Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations
- (2010) Wei Jiang et al. Journal of Chemical Theory and Computation
- Conditions for rapid mixing of parallel and simulated tempering on multimodal distributions
- (2009) Dawn B. Woodard et al. ANNALS OF APPLIED PROBABILITY
- Optimal temperature ladders in replica exchange simulations
- (2009) Robert Denschlag et al. CHEMICAL PHYSICS LETTERS
- Efficiency of exchange schemes in replica exchange
- (2009) Martin Lingenheil et al. CHEMICAL PHYSICS LETTERS
- Error and efficiency of replica exchange molecular dynamics simulations
- (2009) Edina Rosta et al. JOURNAL OF CHEMICAL PHYSICS
- Efficient nonbonded interactions for molecular dynamics on a graphics processing unit
- (2009) Peter Eastman et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Accelerating molecular dynamic simulation on graphics processing units
- (2009) Mark S. Friedrichs et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Temperature random walk sampling of protein configurations
- (2009) Ulrich H.E. Hansmann PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
- Phase transition in the three dimensional Heisenberg spin glass: Finite-size scaling analysis
- (2009) L. A. Fernandez et al. PHYSICAL REVIEW B
- Strengths and weaknesses of parallel tempering
- (2009) J. Machta PHYSICAL REVIEW E
- Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations
- (2009) Daniel K. Shenfeld et al. PHYSICAL REVIEW E
- Rapid equilibrium sampling initiated from nonequilibrium data
- (2009) X. Huang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Efficiency reduction and pseudo-convergence in replica exchange sampling of peptide folding–unfolding equilibria
- (2008) Robert Denschlag et al. CHEMICAL PHYSICS LETTERS
- Optimization of expanded ensemble methods
- (2008) Fernando A. Escobedo et al. JOURNAL OF CHEMICAL PHYSICS
- Calculation of absolute protein-ligand binding free energy using distributed replica sampling
- (2008) Tomas Rodinger et al. JOURNAL OF CHEMICAL PHYSICS
- Statistically optimal analysis of samples from multiple equilibrium states
- (2008) Michael R. Shirts et al. JOURNAL OF CHEMICAL PHYSICS
- Exchange frequency in replica exchange molecular dynamics
- (2008) Daniel Sindhikara et al. JOURNAL OF CHEMICAL PHYSICS
- How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach
- (2008) Hugh Nymeyer Journal of Chemical Theory and Computation
- GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
- (2008) Berk Hess et al. Journal of Chemical Theory and Computation
- Comparison of the serial and parallel algorithms of generalized ensemble simulations: An analytical approach
- (2008) Sanghyun Park PHYSICAL REVIEW E
- Asynchronous replica exchange for molecular simulations
- (2007) Emilio Gallicchio et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
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