A self-learning algorithm for biased molecular dynamics
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September 2010 |
Using sketch-map coordinates to analyze and bias molecular dynamics simulations
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March 2012 |
Secondary active transport mediated by a prokaryotic homologue of ClC Cl- channels
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February 2004 |
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
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February 1977 |
Exact dynamical coarse-graining without time-scale separation
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July 2014 |
Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems
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December 2008 |
Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration
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December 2013 |
Basic ingredients of free energy calculations: A review
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January 2009 |
Atomic-Level Characterization of the Structural Dynamics of Proteins
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October 2010 |
Scalable molecular dynamics with NAMD
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January 2005 |
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
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February 2008 |
Metadynamics with Adaptive Gaussians
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June 2012 |
Unraveling the Mystery of ATP Hydrolysis in Actin Filaments
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September 2014 |
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
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March 1977 |
Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model
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December 2014 |
Metadynamics convergence law in a multidimensional system
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May 2010 |
GROMACS: Fast, flexible, and free
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January 2005 |
Electrostatics of Ion Stabilization in a ClC Chloride Channel Homologue from Escherichia coli
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June 2004 |
A mathematical formalization of the parallel replica dynamics
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January 2012 |
New advances in metadynamics: New advances in metadynamics
- Sutto, Ludovico; Marsili, Simone; Gervasio, Francesco Luigi
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Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 2, Issue 5
https://doi.org/10.1002/wcms.1103
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March 2012 |
GROMACS 3.0: a package for molecular simulation and trajectory analysis
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August 2001 |
From A to B in free energy space
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February 2007 |
Targeting biomolecular flexibility with metadynamics
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April 2010 |
CLC channel function and dysfunction in health and disease
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October 2014 |
Gating the Selectivity Filter in ClC Chloride Channels
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March 2003 |
Sculpting bespoke mountains: Determining free energies with basis expansions
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July 2015 |
Comparison of simple potential functions for simulating liquid water
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July 1983 |
Design, function and structure of a monomeric ClC transporter
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November 2010 |
Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins
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May 2006 |
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins †
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April 1998 |
Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
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November 2008 |
X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity
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January 2002 |
Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States
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March 2001 |
PLUMED 2: New feathers for an old bird
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February 2014 |
Structure of a Eukaryotic CLC Transporter Defines an Intermediate State in the Transport Cycle
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September 2010 |
Accurate Multiple Time Step in Biased Molecular Simulations
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December 2014 |
Free-Energy Landscape for β Hairpin Folding from Combined Parallel Tempering and Metadynamics
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October 2006 |
Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations
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May 2013 |
Well-Tempered Metadynamics Converges Asymptotically
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June 2014 |
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
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August 2004 |
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
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January 2008 |
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
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June 1993 |
A Decade of CLC Chloride Channels: Structure, Mechanism, and Many Unsettled Questions
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June 2000 |
Self-healing Umbrella Sampling: A Non-equilibrium Approach for Quantitative Free Energy Calculations
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July 2006 |
Flux Tempered Metadynamics
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September 2011 |
Nucleotide Regulation of the Structure and Dynamics of G-Actin
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April 2014 |
Ensemble-Biased Metadynamics: A Molecular Simulation Method to Sample Experimental Distributions
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June 2015 |
Designing Free Energy Surfaces That Match Experimental Data with Metadynamics
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May 2015 |
Low temperature asymptotics for quasistationary distributions in a bounded domain
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January 2015 |
Umbrella sampling: Umbrella sampling
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May 2011 |
THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
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October 1992 |
Protein Folding and Ligand-Enzyme Binding from Bias-Exchange Metadynamics Simulations
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January 2012 |
An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids
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August 2000 |
Equilibrium Free Energies from Nonequilibrium Metadynamics
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March 2006 |
CLC Chloride Channels and Transporters: From Genes to Protein Structure, Pathology and Physiology
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January 2008 |
Free Energy Surface Reconstruction from Umbrella Samples Using Gaussian Process Regression
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August 2014 |
Self-Learning Adaptive Umbrella Sampling Method for the Determination of Free Energy Landscapes in Multiple Dimensions
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March 2013 |
Efficient Reconstruction of Complex Free Energy Landscapes by Multiple Walkers Metadynamics †
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March 2006 |
A Time-Independent Free Energy Estimator for Metadynamics
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July 2014 |
Molecular dynamics simulations of biomolecules
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September 2002 |
Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics
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August 2009 |
Statistically optimal analysis of samples from multiple equilibrium states
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September 2008 |
Metadynamics: Metadynamics
- Barducci, Alessandro; Bonomi, Massimiliano; Parrinello, Michele
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Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 1, Issue 5
https://doi.org/10.1002/wcms.31
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February 2011 |
On the convergence improvement in the metadynamics simulations: A Wang-Landau recursion approach
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May 2007 |
A smooth particle mesh Ewald method
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November 1995 |
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
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October 2003 |
Escaping free-energy minima
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September 2002 |
Local elevation: A method for improving the searching properties of molecular dynamics simulation
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December 1994 |
Actin, a Central Player in Cell Shape and Movement
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November 2009 |
Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape
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April 2015 |
A boundary correction algorithm for metadynamics in multiple dimensions
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August 2013 |
A Bias-Exchange Approach to Protein Folding
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May 2007 |
Proton Transport Pathway in the ClC Cl−/H+ Antiporter
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July 2009 |
Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering
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February 2015 |
Adaptive biasing force method for scalar and vector free energy calculations
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April 2008 |
Transition-Tempered Metadynamics: Robust, Convergent Metadynamics via On-the-Fly Transition Barrier Estimation
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August 2014 |
Calculating free energies using average force
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November 2001 |
Nucleotide-dependent conformational states of actin
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July 2009 |
Free energy calculations: Applications to chemical and biochemical phenomena
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November 1993 |
The nature of the globular- to fibrous-actin transition
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January 2009 |