Table of Contents
Introductory Survey H.J.C. Berendsen: Molecular Dynamics Simulations: The Limits and Beyond. I Conformational Dynamics S. Izrailev, S. Stepaniants, B. Isralewitz, D. Kosztin, H. Lu, F. Molnar, W. Wriggers, K. Schulten: Steered Molecular Dynamics.- V. Helms, J.A. McCammon: Conformational Transitions of Proteins from Atomistic Simulations.- M. Eichinger, B. Heymann, H. Heller, H. Grubmüller, P. Tavan: Conformational Dynamics Simulations of Proteins.- P. Deuflhard, M. Dellnitz, O. Junge, C. Schütte: Computation of Essential Molecular Dynamics by Subdivision Techniques.- M.Y. Tolstorukov, K.M. Virnik: Mathematical Model of the Nucleic Acids Conformatinal Transitions with Hysteresis over Hydration-Dehydration Cycle. II Thermodynamic Modelling J. Hermans, G. Mann, L. Wang, L. Zhang: Simulation Studies of Protein- Ligand Interactions.- A.E. Mark, H. Schäfer, H. Liu, W. van Gunsteren: Estimating Relative Free Energies from a Single Simulation of the Initial State.- K. Kuczera: Exploration of Peptide Free Energy Surfaces.- J. Antosiewicz, E. Blachut- Okrasinska, T. Grycuk, J.M. Briggs, S.T. Wlodek, B. Lesyng, J.A. McCammon: Prediction of pK(a)s of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute- Solvent System.- J.E. Straub, I. Andricioaei: Exploiting Tsallis Statistics.- A. Neumaier, S. Dallwig, W. Huyer, H. Schichl: New Techniques for the Construction of Residue Potentials for Protein Folding. III Enhanced Time-Stepping Algorithms T. Schlick: Some Failures and Successes of Long-Timestep Approaches to Biomolecular Simulations.- R. Elber, B. Roux, R. Olender: Application of a Shastic Path Integral Approach to the Computation of an Optimal Path and Ensemble of Trjectories.- U.M. Ascher, S. Reich: On Some Difficulties in Integrating Highly Oscillatory Hamiltonian Systems.- B.J. Berne: Molecular Dynamics in Systems with Multiple Time Scales: Reference System Propagator Algorithms.- R.D. Skeel, J.A. Izaguirre: The Five Femtosecond Time StepBarrier.- D. Janezic, F. Merzel: Long Time Step MD Simulations using Split Integration Symplectic Method.- B.J. Leimkuhler: Comparison of Geometric Integrators for Rigid Body Simulation. IV Quantum-Classical Simulations P. Jungwirth, R.B. Gerber: New Methods in Quantum Molecular Dynamics of Large Polyatomic Systems.- C. Schütte, F. Bornemann: Approximation Properties and Limits of the Quantum-Classical Molecular Dynamics Model.- P. Nettesheim, C. Schütte: Numerical Integrators for Quantum-Classical Molecular Dynamics.- P. Nettesheim, S. Reich: Symplectic Multiple-Time-Stepping Integrators for Quantum-Classical Molecular Dynamics.- M. Hochbruck, C. Lubich: A Bunch of Time Integrators for Quantum/Classical Molecular Dynamics.- R.J. Meier: Applications of Ab-Initio Molecular Dynamics Simulations in Chemistry and Polymer Science.- S.V. Izvekov: Polarons of Molecular Crystal Model by Nonlocal Dynamical Coherent Potential Method. V Parallel Force Field Evaluation J.A. Board Jr., c.W. Humphres, C.G. Lambert, W.T. Rankin, A.Y. Toukmaji: Ewald and Multipole Methods for Periodic N-body Problems.- J.C. Phillips, R. Brunner, A. Shinozaki, M. Bhandarkar, N. Krawetz, A. Gursoy, L. Kale, R.D. Skeel, K. Schulten: Avoiding Algorithmic Obfuscation in a Message- Driven Parallel MD Code.- D. Okunbor, R. Murty: Parallel Molecular Dynamics Using Force Decomposition.
