Computational Molecular Dynamics: Challenges, Methods, Ideas

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.

Inhalt

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 Stochastic 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.