标题
Enhanced sampling in molecular dynamics
作者
关键词
-
出版物
JOURNAL OF CHEMICAL PHYSICS
Volume 151, Issue 7, Pages 070902
出版商
AIP Publishing
发表日期
2019-08-16
DOI
10.1063/1.5109531
参考文献
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- (2019) Yue-Yu Zhang et al. JOURNAL OF CHEMICAL PHYSICS
- Dynamic Electric Field Complicates Chemical Reactions in Solutions
- (2019) Yaokun Lei et al. Journal of Physical Chemistry Letters
- Molecular dynamics simulation, ab initio calculation, and size-selected anion photoelectron spectroscopy study of initial hydration processes of calcium chloride
- (2018) Zhili He et al. JOURNAL OF CHEMICAL PHYSICS
- Refining Collective Coordinates and Improving Free Energy Representation in Variational Enhanced Sampling
- (2018) Yi Isaac Yang et al. Journal of Chemical Theory and Computation
- Accelerated Enveloping Distribution Sampling: Enabling Sampling of Multiple End States while Preserving Local Energy Minima
- (2018) Jan Walther Perthold et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Collective Variables from Local Fluctuations
- (2018) Dan Mendels et al. Journal of Physical Chemistry Letters
- Integrated tempering enhanced sampling method as the infinite switching limit of simulated tempering
- (2018) Zhiyi You et al. JOURNAL OF CHEMICAL PHYSICS
- Metadynamics with Discriminants: A Tool for Understanding Chemistry
- (2018) GiovanniMaria Piccini et al. Journal of Chemical Theory and Computation
- Folding a small protein using harmonic linear discriminant analysis
- (2018) Dan Mendels et al. JOURNAL OF CHEMICAL PHYSICS
- Combining Metadynamics and Integrated Tempering Sampling
- (2018) Yi Isaac Yang et al. Journal of Physical Chemistry Letters
- A variational conformational dynamics approach to the selection of collective variables in metadynamics
- (2017) James McCarty et al. JOURNAL OF CHEMICAL PHYSICS
- Transition path sampling of rare events by shooting from the top
- (2017) Hendrik Jung et al. JOURNAL OF CHEMICAL PHYSICS
- Determining Protein Folding Pathway and Associated Energetics through Partitioned Integrated-Tempering-Sampling Simulation
- (2017) Qiang Shao et al. Journal of Chemical Theory and Computation
- Coarse graining from variationally enhanced sampling applied to the Ginzburg–Landau model
- (2017) Michele Invernizzi et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Rich Dynamics Underlying Solution Reactions Revealed by Sampling and Data Mining of Reactive Trajectories
- (2017) Jun Zhang et al. ACS Central Science
- Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint
- (2016) Omar Valsson et al. Annual Review of Physical Chemistry
- Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling
- (2016) Y. Isaac Yang et al. JOURNAL OF CHEMICAL PHYSICS
- Hydration of potassium iodide dimer studied by photoelectron spectroscopy and ab initio calculations
- (2016) Ren-Zhong Li et al. JOURNAL OF CHEMICAL PHYSICS
- Initial hydration behavior of sodium iodide dimer: photoelectron spectroscopy and ab initio calculations
- (2016) Ren-Zhong Li et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Spectral gap optimization of order parameters for sampling complex molecular systems
- (2016) Pratyush Tiwary et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- From Thermodynamics to Kinetics: Enhanced Sampling of Rare Events
- (2015) Lijiang Yang et al. ACCOUNTS OF CHEMICAL RESEARCH
- Dynamics and Kinetics Study of “In-Water” Chemical Reactions by Enhanced Sampling of Reactive Trajectories
- (2015) Jun Zhang et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Conformational Preadjustment in Aqueous Claisen Rearrangement Revealed by SITS-QM/MM MD Simulations
- (2015) Jun Zhang et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Understanding the microsolvation of salts in molecular clusters
- (2014) Cheng-Wen Liu et al. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
- A Time-Independent Free Energy Estimator for Metadynamics
- (2014) Pratyush Tiwary et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Probing Sequence Dependence of Folding Pathway of α-Helix Bundle Proteins through Free Energy Landscape Analysis
- (2014) Qiang Shao JOURNAL OF PHYSICAL CHEMISTRY B
- Stable Salt–Water Cluster Structures Reflect the Delicate Competition between Ion–Water and Water–Water Interactions
- (2014) Cheng-Wen Liu et al. JOURNAL OF PHYSICAL CHEMISTRY B
- How Quickly Can a β-Hairpin Fold from Its Transition State?
- (2014) Beatrice N. Markiewicz et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Variational Approach to Enhanced Sampling and Free Energy Calculations
- (2014) Omar Valsson et al. PHYSICAL REVIEW LETTERS
- Dynamics of spontaneous flipping of a mismatched base in DNA duplex
- (2014) Y. Yin et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Infinite swapping replica exchange molecular dynamics leads to a simple simulation patch using mixture potentials
- (2013) Jianfeng Lu et al. JOURNAL OF CHEMICAL PHYSICS
- Identification of slow molecular order parameters for Markov model construction
- (2013) Guillermo Pérez-Hernández et al. JOURNAL OF CHEMICAL PHYSICS
- Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
- (2013) Christian R. Schwantes et al. Journal of Chemical Theory and Computation
- Microsolvation of LiI and CsI in Water: Anion Photoelectron Spectroscopy and ab initio Calculations
- (2013) Ren-Zhong Li et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- The relative helix and hydrogen bond stability in the B domain of protein A as revealed by integrated tempering sampling molecular dynamics simulation
- (2011) Qiang Shao et al. JOURNAL OF CHEMICAL PHYSICS
- Metadynamics
- (2011) Alessandro Barducci et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Exchange Often and Properly in Replica Exchange Molecular Dynamics
- (2010) Daniel J. Sindhikara et al. Journal of Chemical Theory and Computation
- Temperature Dependence of Hydrogen-Bond Stability in β-Hairpin Structures
- (2010) Qiang Shao et al. Journal of Chemical Theory and Computation
- Effects of Turn Stability and Side-Chain Hydrophobicity on the Folding of β-Structures
- (2010) Qiang Shao et al. JOURNAL OF MOLECULAR BIOLOGY
- A selective integrated tempering method
- (2009) Lijiang Yang et al. JOURNAL OF CHEMICAL PHYSICS
- Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations
- (2009) Edina Rosta et al. Journal of Chemical Theory and Computation
- Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics
- (2009) M. Bonomi et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Using the local elevation method to construct optimized umbrella sampling potentials: Calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water
- (2009) Halvor S. Hansen et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Transition Path Theory for Markov Jump Processes
- (2009) Philipp Metzner et al. MULTISCALE MODELING & SIMULATION
- Self-adaptive enhanced sampling in the energy and trajectory spaces: Accelerated thermodynamics and kinetic calculations
- (2008) Yi Qin Gao JOURNAL OF CHEMICAL PHYSICS
- An integrate-over-temperature approach for enhanced sampling
- (2008) Yi Qin Gao JOURNAL OF CHEMICAL PHYSICS
- Exchange frequency in replica exchange molecular dynamics
- (2008) Daniel Sindhikara et al. JOURNAL OF CHEMICAL PHYSICS
- Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
- (2008) Alessandro Barducci et al. PHYSICAL REVIEW LETTERS
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