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EBOOK
Title Free energy calculations : theory and applications in chemistry and biology / Ch. Chipot, A. Pohorille (eds.).
Imprint Berlin : Springer, 2007.

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 OHIOLINK SPRINGER EBOOKS    ONLINE  
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LOCATION CALL # STATUS MESSAGE
 OHIOLINK SPRINGER EBOOKS    ONLINE  
View online
Series Springer series in chemical physics, 0172-6218 ; 86
Springer series in chemical physics ; 86. 0172-6218
Subject Linear free energy relationship -- Computer simulation.
Alt Name Pohorille, A. (Andrew)
Chipot, Ch. (Christophe)
Description 1 online resource (xviii, 517 pages) : illustrations (some color).
Bibliography Note Includes bibliographical references and index.
Contents Cover -- Contents -- 1 Introduction -- 1.1 Historical Backdrop -- 1.1.1 The Pioneers of Free Energy Calculations -- 1.1.2 Escaping from Boltzmann Sampling -- 1.1.3 Early Successes and Failures of Free Energy Calculations -- 1.1.4 Characterizing, Understanding, and Improving Free Energy Calculations -- 1.2 The Density of States -- 1.2.1 Mathematical Formalism -- 1.2.2 Application: MC Simulation in the Microcanonical Ensemble -- 1.3 Free Energy -- 1.3.1 Basic Approaches to Free Energy Calculations -- 1.4 Ergodicity, Quasi-nonergodicity and Enhanced Sampling -- References -- 2 Calculating Free Energy Differences Using Perturbation Theory -- 2.1 Introduction -- 2.2 The Perturbation Formalism -- 2.3 Interpretation of the Free Energy Perturbation Equation -- 2.4 Cumulant Expansion of the Free Energy -- 2.5 Two Simple Applications of Perturbation Theory -- 2.5.1 Charging a Spherical Particle -- 2.5.2 Dipolar Solutes at an Aqueous Interface -- 2.6 How to Deal with Large Perturbations -- 2.7 A Pictorial Representation of Free Energy Perturbation -- 2.8 'Alchemical Transformations' -- 2.8.1 Order Parameters -- 2.8.2 Creation and Annihilation -- 2.8.3 Free Energies of Binding -- 2.8.4 The Single-Topology Paradigm -- 2.8.5 The Dual-Topology Paradigm -- 2.8.6 Algorithm of an FEP Point-Mutation Calculation -- 2.9 Improving the Efficiency of FEP -- 2.9.1 Combining Forward and Backward Transformations -- 2.9.2 Hamiltonian Hopping -- 2.9.3 Modeling Probability Distributions -- 2.10 Calculating Free Energy Contributions -- 2.10.1 Estimating Energies and Entropies -- 2.10.2 How Relevant are Free Energy Contributions? -- 2.11 Summary -- References -- 3 Methods Based on Probability Distributions and Histograms -- 3.1 Introduction -- 3.2 Histogram Reweighting -- 3.2.1 Free Energies from Histograms -- 3.2.2 Ferrenberg-Swendsen Reweighting and WHAM -- 3.3 Basic Stratification and Importance Sampling -- 3.3.1 Stratification -- 3.3.2 Importance Sampling -- 3.3.3 Importance Sampling and Stratification with WHAM -- 3.4 Flat-Histogram Methods -- 3.4.1 Theoretical Basis -- 3.4.2 The Multicanonical Method -- 3.4.3 Wang-Landau Sampling -- 3.4.4 Transition-Matrix Estimators -- 3.4.5 Implementation Issues -- 3.5 Order Parameters, Reaction Coordinates, and Extended Ensembles -- References -- 4 Thermodynamic Integration Using Constrained and Unconstrained Dynamics -- 4.1 Introduction -- 4.2 Methods for Constrained and Unconstrained Simulations -- 4.3 Generalized Coordinates and Lagrangian Formulation -- 4.3.1 Generalized Coordinates -- 4.4 The Derivative of the Free Energy -- 4.4.1 Discussion of (4.15) -- 4.5 The Potential of Mean Constraint Force -- 4.5.1 Constrained Simulation -- 4.5.2 The Fixman Potential -- 4.5.3 The Potential of Mean Constraint Force -- 4.5.4 A More Concise Expression -- 4.6 The Adaptive Biasing Force Method -- 4.6.1 The Derivative of the Free Energy -- 4.6.2 Numerical Calculation of the Time Derivatives.
Summary Presenting an account of the concepts that underly different approaches devised for the determination of free energies, this book aims to give the reader, an insight into the theoretical and computational foundations of the subject. It is aimed at students and researchers having a background in chemistry, physics, engineering and physical biology.
Note Print version record.
ISBN 9783540384472 (Print)
3540384472 (Print)
9783540384489 (Online)
3540384480 (Online)
1280745339
9781280745331
6610745331
9786610745333
ISBN/ISSN 10.1007/978-3-540-38448-9
OCLC # 85376028
Additional Format Print version: Free energy calculations. Berlin ; New York : Springer, 2007 9783540384472 3540384472 (OCoLC)79447449


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