Related references
Note: Only part of the references are listed.Convergence of single-step free energy perturbation
Stefan Boresch et al.
MOLECULAR PHYSICS (2017)
Stiff Spring Approximation Revisited: Inertial Effects in Nonequilibrium Trajectories
Mostafa Nategholeslam et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2017)
Access and Binding of H2S to Hemeproteins: The Case of HbI of Lucina pectinata
Fernando M. Boubeta et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2016)
Number of trials required to estimate a free-energy difference, using fluctuation relations
Nicole Yunger Halpern et al.
PHYSICAL REVIEW E (2016)
Improving Efficiency in SMD Simulations Through a Hybrid Differential Relaxation Algorithm
Claudia L. Ramirez et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation
Yinglong Miao et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Looking for Some Free Energy? Call JEFREE (...)
Mirco Zerbetto et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2014)
Hydrophobic Effect Drives Oxygen Uptake in Myoglobin via Histidine E7
Leonardo Boechi et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2013)
Local Sampling in Steered Monte Carlo Simulations Decreases Dissipation and Enhances Free Energy Estimates via Nonequilibrium Work Theorems
Riccardo Chelli
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Estimation of Free-Energy Differences from Computed Work Distributions: An Application of Jarzynski's Equality
Ignacia Echeverria et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
Protein dynamics and ligand migration interplay as studied by computer simulation
Pau Arroyo-Manez et al.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2011)
Exploiting Configurational Freezing in Nonequilibrium Monte Carlo Simulations
Paolo Nicolini et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
A High-Throughput Steered Molecular Dynamics Study on the Free Energy Profile of Ion Permeation through Gramicidin A
Toni Giorgino et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Comparing and Combining Implicit Ligand Sampling with Multiple Steered Molecular Dynamics to Study Ligand Migration Processes in Heme Proteins
Flavio Forti et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)
Free energy evaluation of the p53-Mdm2 complex from unbinding work measured by dynamic force spectroscopy
Anna Rita Bizzarri et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2011)
Improving Free-Energy Estimates from Unidirectional Work Measurements: Theory and Experiment
Matteo Palassini et al.
PHYSICAL REVIEW LETTERS (2011)
Equalities and Inequalities: Irreversibility and the Second Law of Thermodynamics at the Nanoscale
Christopher Jarzynski
ANNUAL REVIEW OF CONDENSED MATTER PHYSICS, VOL 2 (2011)
Sulfide Binding Properties of Truncated Hemoglobins
Francesco P. Nicoletti et al.
BIOCHEMISTRY (2010)
Energy dissipation asymmetry in the non equilibrium folding/unfolding of the single molecule alanine decapeptide
Piero Procacci et al.
CHEMICAL PHYSICS (2010)
Adaptive Steered Molecular Dynamics of the Long-Distance Unfolding of Neuropeptide Y
Gungor Ozer et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Hummer and Szabo-like Potential of Mean Force Estimator for Bidirectional Nonequilibrium Pulling Experiments/Simulations
Paolo Nicolini et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Good Practices in Free-Energy Calculations
Andrew Pohorille et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Fluctuation Theorem Applied to F1-ATPase
Kumiko Hayashi et al.
PHYSICAL REVIEW LETTERS (2010)
Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages
David D. L. Minh et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
Comparative energy measurements in single molecule interactions
W. Liu et al.
BIOPHYSICAL JOURNAL (2008)
Statistically optimal analysis of samples from multiple equilibrium states
Michael R. Shirts et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
Springs and speeds in free energy reconstruction from irreversible single-molecule pulling experiments
David D. L. Minh et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Escorted free energy simulations: Improving convergence by reducing dissipation
Suriyanarayanan Vaikuntanathan et al.
PHYSICAL REVIEW LETTERS (2008)
Optimized free energies from bidirectional single-molecule force spectroscopy
David D. L. Minh et al.
PHYSICAL REVIEW LETTERS (2008)
Experimental free energy surface reconstruction from single-molecule force spectroscopy using Jarzynski's equality
Nolan C. Harris et al.
PHYSICAL REVIEW LETTERS (2007)
Single molecule pulling with large time steps
Harald Oberhofer et al.
PHYSICAL REVIEW E (2007)
Optimal finite-time processes in stochastic thermodynamics
Tim Schmiedl et al.
PHYSICAL REVIEW LETTERS (2007)
Work distribution for the adiabatic compression of a dilute and interacting classical gas
Gavin E. Crooks et al.
PHYSICAL REVIEW E (2007)
Free energy calculations with non-equilibrium methods: applications of the Jarzynski relationship
Hui Xiong et al.
THEORETICAL CHEMISTRY ACCOUNTS (2006)
Rare events and the convergence of exponentially averaged work values
C Jarzynski
PHYSICAL REVIEW E (2006)
Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain
DQ Zhang et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Exploring the free-energy landscape of a short peptide using an average force -: art. no. 244906
C Chipot et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Phase-space overlap measures. II. Design and implementation of staging methods for free-energy calculations
D Wu et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Phase-space overlap measures. I. Fail-safe bias detection in free energies calculated by molecular simulation
D Wu et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
An experimental test of the Jarzynski equality in a mechanical experiment
F Douarche et al.
EUROPHYSICS LETTERS (2005)
Application of steered molecular dynamics (SMD) to study DNA-drug complexes and probing helical propensity of amino acids
M Orzechowski et al.
JOURNAL OF PHYSICS-CONDENSED MATTER (2005)
Mechanical unfolding of RNA hairpins
C Hyeon et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration
MR Shirts et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Calculating potentials of mean force from steered molecular dynamics simulations
S Park et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Asymmetric bias in free-energy perturbation measurements using two Hamiltonian-based models
D Wu et al.
PHYSICAL REVIEW E (2004)
Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems
FM Ytreberg et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Model for small-sample bias of free-energy calculations applied to Gaussian-distributed nonequilibrium work measurements
D Wu et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements
J Gore et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods
MR Shirts et al.
PHYSICAL REVIEW LETTERS (2003)
Theory of a systematic computational error in free energy differences
DM Zuckerman et al.
PHYSICAL REVIEW LETTERS (2002)
Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality
J Liphardt et al.
SCIENCE (2002)
Overcoming finite-sampling errors in fast-switching free-energy estimates: extrapolative analysis of a molecular system
DM Zuckerman et al.
CHEMICAL PHYSICS LETTERS (2002)
Accuracy of free-energy perturbation calculations in molecular simulation. II. Heuristics
ND Lu et al.
JOURNAL OF CHEMICAL PHYSICS (2001)
Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling
ND Lu et al.
JOURNAL OF CHEMICAL PHYSICS (2001)
Fast-growth thermodynamic integration: Error and efficiency analysis
G Hummer
JOURNAL OF CHEMICAL PHYSICS (2001)
Free energy reconstruction from nonequilibrium single-molecule pulling experiments
G Hummer et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
Path-ensemble averages in systems driven far from equilibrium
GE Crooks
PHYSICAL REVIEW E (2000)