Ebook: Computational Molecular Dynamics: Challenges, Methods, Ideas: Proceedings of the 2nd International Symposium on Algorithms for Macromolecular Modelling, Berlin, May 21–24, 1997

On May 21-24, 1997 the Second International Symposium on Algorithms for Macromolecular Modelling was held at the Konrad Zuse Zentrum in Berlin. The event brought together computational scientists in fields like biochemistry, biophysics, physical chemistry, or statistical physics and numerical analysts as well as computer scientists working on the advancement of algorithms, for a total of over 120 participants from 19 countries. In the course of the symposium, the speakers agreed to produce a representative volume that combines survey articles and original papers (all refereed) to give an impression of the present state of the art of Molecular Dynamics.
The 29 articles of the book reflect the main topics of the Berlin meeting which were i) Conformational Dynamics, ii) Thermodynamic Modelling, iii) Advanced Time-Stepping Algorithms, iv) Quantum-Classical Simulations and Fast Force Field and v) Fast Force Field Evaluation.

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On May 21-24, 1997 the Second International Symposium on Algorithms for Macromolecular Modelling was held at the Konrad Zuse Zentrum in Berlin. The event brought together computational scientists in fields like biochemistry, biophysics, physical chemistry, or statistical physics and numerical analysts as well as computer scientists working on the advancement of algorithms, for a total of over 120 participants from 19 countries. In the course of the symposium, the speakers agreed to produce a representative volume that combines survey articles and original papers (all refereed) to give an impression of the present state of the art of Molecular Dynamics.
The 29 articles of the book reflect the main topics of the Berlin meeting which were i) Conformational Dynamics, ii) Thermodynamic Modelling, iii) Advanced Time-Stepping Algorithms, iv) Quantum-Classical Simulations and Fast Force Field and v) Fast Force Field Evaluation.

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On May 21-24, 1997 the Second International Symposium on Algorithms for Macromolecular Modelling was held at the Konrad Zuse Zentrum in Berlin. The event brought together computational scientists in fields like biochemistry, biophysics, physical chemistry, or statistical physics and numerical analysts as well as computer scientists working on the advancement of algorithms, for a total of over 120 participants from 19 countries. In the course of the symposium, the speakers agreed to produce a representative volume that combines survey articles and original papers (all refereed) to give an impression of the present state of the art of Molecular Dynamics.
The 29 articles of the book reflect the main topics of the Berlin meeting which were i) Conformational Dynamics, ii) Thermodynamic Modelling, iii) Advanced Time-Stepping Algorithms, iv) Quantum-Classical Simulations and Fast Force Field and v) Fast Force Field Evaluation.
Content:
Front Matter....Pages N1-XI
Front Matter....Pages 1-1
Molecular Dynamics Simulations: The Limits and Beyond....Pages 3-36
Front Matter....Pages 37-37
Steered Molecular Dynamics....Pages 39-65
Conformational Transitions of Proteins from Atomistic Simulations....Pages 66-77
Conformational Dynamics Simulations of Proteins....Pages 78-97
Computation of Essential Molecular Dynamics by Subdivision Techniques....Pages 98-115
Mathematical Model of the Nucleic Acids Conformational Transitions with Hysteresis over Hydration—Dehydration Cycle....Pages 116-126
Front Matter....Pages 127-127
Simulation Studies of Protein-Ligand Interactions....Pages 129-148
Estimating Relative Free Energies from a Single Simulation of the Initial State....Pages 149-162
Exploration of Peptide Free Energy Surfaces....Pages 163-175
Prediction of pKas of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute-Solvent System....Pages 176-196
Exploiting Tsallis Statistics....Pages 197-211
New Techniques for the Construction of Residue Potentials for Protein Folding....Pages 212-224
Front Matter....Pages 225-225
Some Failures and Successes of Long-Timestep Approaches to Biomolecular Simulations....Pages 227-262
Application of a Stochastic Path Integral Approach to the Computations of an Optimal Path and Ensembles of Trajectories....Pages 263-280
On Some Difficulties in Integrating Highly Oscillatory Hamiltonian Systems....Pages 281-296
Molecular Dynamics in Systems with Multiple Time Scales: Reference System Propagator Algorithms....Pages 297-317
The Five Femtosecond Time Step Barrier....Pages 318-331
Long Time Step MD Simulations Using Split Integration Symplectic Method....Pages 332-348
Comparison of Geometric Integrators for Rigid Body Simulation....Pages 349-362
Front Matter....Pages 363-363
New Methods in Quantum Molecular Dynamics of Large Polyatomic Systems....Pages 365-379
Front Matter....Pages 363-363
Approximation Properties and Limits of the Quantum-Classical Molecular Dynamics Model....Pages 380-395
Numerical Integrators for Quantum-Classical Molecular Dynamics....Pages 396-411
Symplectic Multiple-Time-Stepping Integrators for Quantum-Classical Molecular Dynamics....Pages 412-420
A Bunch of Time Integrators for Quantum/Classical Molecular Dynamics....Pages 421-432
Applications of Ab-Initio Molecular Dynamics Simulations in Chemistry and Polymer Science....Pages 433-441
Polarons of Molecular Crystal Model by Nonlocal Dynamical Coherent Potential Method....Pages 442-456
Front Matter....Pages 457-457
Ewald and Multipole Methods for Periodic N-Body Problems....Pages 459-471
Avoiding Algorithmic Obfuscation in a Message-Driven Parallel MD Code....Pages 472-482
Parallel Molecular Dynamics Using Force Decomposition....Pages 483-494
Back Matter....Pages 495-498

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On May 21-24, 1997 the Second International Symposium on Algorithms for Macromolecular Modelling was held at the Konrad Zuse Zentrum in Berlin. The event brought together computational scientists in fields like biochemistry, biophysics, physical chemistry, or statistical physics and numerical analysts as well as computer scientists working on the advancement of algorithms, for a total of over 120 participants from 19 countries. In the course of the symposium, the speakers agreed to produce a representative volume that combines survey articles and original papers (all refereed) to give an impression of the present state of the art of Molecular Dynamics.
The 29 articles of the book reflect the main topics of the Berlin meeting which were i) Conformational Dynamics, ii) Thermodynamic Modelling, iii) Advanced Time-Stepping Algorithms, iv) Quantum-Classical Simulations and Fast Force Field and v) Fast Force Field Evaluation.
Content:
Front Matter....Pages N1-XI
Front Matter....Pages 1-1
Molecular Dynamics Simulations: The Limits and Beyond....Pages 3-36
Front Matter....Pages 37-37
Steered Molecular Dynamics....Pages 39-65
Conformational Transitions of Proteins from Atomistic Simulations....Pages 66-77
Conformational Dynamics Simulations of Proteins....Pages 78-97
Computation of Essential Molecular Dynamics by Subdivision Techniques....Pages 98-115
Mathematical Model of the Nucleic Acids Conformational Transitions with Hysteresis over Hydration—Dehydration Cycle....Pages 116-126
Front Matter....Pages 127-127
Simulation Studies of Protein-Ligand Interactions....Pages 129-148
Estimating Relative Free Energies from a Single Simulation of the Initial State....Pages 149-162
Exploration of Peptide Free Energy Surfaces....Pages 163-175
Prediction of pKas of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute-Solvent System....Pages 176-196
Exploiting Tsallis Statistics....Pages 197-211
New Techniques for the Construction of Residue Potentials for Protein Folding....Pages 212-224
Front Matter....Pages 225-225
Some Failures and Successes of Long-Timestep Approaches to Biomolecular Simulations....Pages 227-262
Application of a Stochastic Path Integral Approach to the Computations of an Optimal Path and Ensembles of Trajectories....Pages 263-280
On Some Difficulties in Integrating Highly Oscillatory Hamiltonian Systems....Pages 281-296
Molecular Dynamics in Systems with Multiple Time Scales: Reference System Propagator Algorithms....Pages 297-317
The Five Femtosecond Time Step Barrier....Pages 318-331
Long Time Step MD Simulations Using Split Integration Symplectic Method....Pages 332-348
Comparison of Geometric Integrators for Rigid Body Simulation....Pages 349-362
Front Matter....Pages 363-363
New Methods in Quantum Molecular Dynamics of Large Polyatomic Systems....Pages 365-379
Front Matter....Pages 363-363
Approximation Properties and Limits of the Quantum-Classical Molecular Dynamics Model....Pages 380-395
Numerical Integrators for Quantum-Classical Molecular Dynamics....Pages 396-411
Symplectic Multiple-Time-Stepping Integrators for Quantum-Classical Molecular Dynamics....Pages 412-420
A Bunch of Time Integrators for Quantum/Classical Molecular Dynamics....Pages 421-432
Applications of Ab-Initio Molecular Dynamics Simulations in Chemistry and Polymer Science....Pages 433-441
Polarons of Molecular Crystal Model by Nonlocal Dynamical Coherent Potential Method....Pages 442-456
Front Matter....Pages 457-457
Ewald and Multipole Methods for Periodic N-Body Problems....Pages 459-471
Avoiding Algorithmic Obfuscation in a Message-Driven Parallel MD Code....Pages 472-482
Parallel Molecular Dynamics Using Force Decomposition....Pages 483-494
Back Matter....Pages 495-498
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