Computational Molecular Dynamics: Challenges, Methods, Ideas

Introductory Survey.- Molecular Dynamics Simulations: The Limits and Beyond.- I Conformational Dynamics.- Steered Molecular Dynamics.- Conformational Transitions of Proteins from Atomistic Simulations.- Conformational Dynamics Simulations of Proteins.- Computation of Essential Molecular Dynamics by Subdivision Techniques.- Mathematical Model of the Nucleic Acids Conformational Transitions with Hysteresis over Hydration-Dehydration Cycle.- II Thermodynamic Modelling.- Simulation Studies of Protein-Ligand Interactions.- Estimating Relative Free Energies from a Single Simulation of the Initial State.- Exploration of Peptide Free Energy Surfaces.- Prediction of pKas of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute-Solvent System.- Exploiting Tsallis Statistics.- New Techniques for the Construction of Residue Potentials for Protein Folding.- III Enhanced Time-Stepping Algorithms.- Some Failures and Successes of Long-Timestep Approaches to Biomolecular Simulations.- Application of a Stochastic Path Integral Approach to the Computations of an Optimal Path and Ensembles of Trajectories.- On Some Difficulties in Integrating Highly Oscillatory Hamiltonian Systems.- Molecular Dynamics in Systems with Multiple Time Scales: Reference System Propagator Algorithms.- The Five Femtosecond Time Step Barrier.- Long Time Step MD Simulations Using Split Integration Symplectic Method.- Comparison of Geometric Integrators for Rigid Body Simulation.- IV Quantum-Classical Simulations.- New Methods in Quantum Molecular Dynamics of Large Polyatomic Systems.- Approximation Properties and Limits of the Quantum-Classical Molecular Dynamics Model.- Numerical Integrators for Quantum-Classical Molecular Dynamics.- Symplectic Multiple-Time-Stepping Integrators for Quantum-Classical Molecular Dynamics.- A Bunch of Time Integrators for Quantum/Classical Molecular Dynamics.- Applications of Ab-Initio Molecular Dynamics Simulations in Chemistry and Polymer Science.- Polarons of Molecular Crystal Model by Nonlocal Dynamical Coherent Potential Method.- V Parallel Force Field Evaluation.- Ewald and Multipole Methods for PeriodicN-Body Problems.- Avoiding Algorithmic Obfuscation in a Message-Driven Parallel MD Code.- Parallel Molecular Dynamics Using Force Decomposition.