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Computational Molecular Dynamics: Challenges, Methods, Ideas

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Table of Contents

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    Book Overview
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    Chapter 1 Molecular Dynamics Simulations: The Limits and Beyond
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    Chapter 2 Steered Molecular Dynamics
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    Chapter 3 Conformational Transitions of Proteins from Atomistic Simulations
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    Chapter 4 Conformational Dynamics Simulations of Proteins
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    Chapter 5 Computation of Essential Molecular Dynamics by Subdivision Techniques
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    Chapter 6 Mathematical Model of the Nucleic Acids Conformational Transitions with Hysteresis over Hydration—Dehydration Cycle
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    Chapter 7 Simulation Studies of Protein-Ligand Interactions
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    Chapter 8 Estimating Relative Free Energies from a Single Simulation of the Initial State
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    Chapter 9 Exploration of Peptide Free Energy Surfaces
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    Chapter 10 Prediction of pK a s of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute-Solvent System
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    Chapter 11 Exploiting Tsallis Statistics
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    Chapter 12 New Techniques for the Construction of Residue Potentials for Protein Folding
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    Chapter 13 Some Failures and Successes of Long-Timestep Approaches to Biomolecular Simulations
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    Chapter 14 Application of a Stochastic Path Integral Approach to the Computations of an Optimal Path and Ensembles of Trajectories
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    Chapter 15 On Some Difficulties in Integrating Highly Oscillatory Hamiltonian Systems
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    Chapter 16 Molecular Dynamics in Systems with Multiple Time Scales: Reference System Propagator Algorithms
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    Chapter 17 The Five Femtosecond Time Step Barrier
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    Chapter 18 Long Time Step MD Simulations Using Split Integration Symplectic Method
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    Chapter 19 Comparison of Geometric Integrators for Rigid Body Simulation
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    Chapter 20 New Methods in Quantum Molecular Dynamics of Large Polyatomic Systems
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    Chapter 21 Approximation Properties and Limits of the Quantum-Classical Molecular Dynamics Model
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    Chapter 22 Numerical Integrators for Quantum-Classical Molecular Dynamics
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    Chapter 23 Symplectic Multiple-Time-Stepping Integrators for Quantum-Classical Molecular Dynamics
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    Chapter 24 A Bunch of Time Integrators for Quantum/Classical Molecular Dynamics
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    Chapter 25 Applications of Ab-Initio Molecular Dynamics Simulations in Chemistry and Polymer Science
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    Chapter 26 Polarons of Molecular Crystal Model by Nonlocal Dynamical Coherent Potential Method
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    Chapter 27 Ewald and Multipole Methods for Periodic N-Body Problems
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    Chapter 28 Avoiding Algorithmic Obfuscation in a Message-Driven Parallel MD Code
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    Chapter 29 Parallel Molecular Dynamics Using Force Decomposition
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Computational Molecular Dynamics: Challenges, Methods, Ideas
Published by
Springer Berlin Heidelberg, December 2012
DOI 10.1007/978-3-642-58360-5
978-3-54-063242-9, 978-3-64-258360-5

Deuflhard, Peter, Hermans, Jan, Leimkuhler, Benedict, Mark, Alan E., Reich, Sebastian, Skeel, Robert D.

Mendeley readers

The data shown below were compiled from readership statistics for 267 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
India 4 1%
United Kingdom 3 1%
Argentina 2 <1%
France 2 <1%
Italy 2 <1%
Spain 2 <1%
United States 2 <1%
Czechia 1 <1%
Brazil 1 <1%
Other 6 2%
Unknown 242 91%

Demographic breakdown

Readers by professional status Count As %
Researcher 63 24%
Student > Ph. D. Student 62 23%
Student > Master 36 13%
Professor 21 8%
Student > Bachelor 18 7%
Other 51 19%
Unknown 16 6%
Readers by discipline Count As %
Chemistry 72 27%
Engineering 46 17%
Physics and Astronomy 38 14%
Agricultural and Biological Sciences 30 11%
Materials Science 22 8%
Other 38 14%
Unknown 21 8%