Computational Molecular Dynamics: Challenges, Methods, Ideas

Table of Contents

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