VIII Preface the force-row interleaving method,and the force-stripped row method)in the context of a benchmark test problem. August 31,1998 Peter Deufthard Jan Hermans Benedict Leimkuhler Alan E.Mark Sebastian Reich Robert D.Skeel
Table of Contents Introductory Survey Molecular Dynamics Simulations:The Limits and Beyond............ 3 Herman J.C.Berendsen Conformational Dynamics Steered Molecular Dynamics...................................... 39 Sergei Izrailev,Sergey Stepaniants,Barry Isralewitz,Dorina Kosztin,Hui Lu,Ferenc Molnar,Willy Wriggers,Klaus Schulten Conformational Transitions of Proteins from Atomistic Simulations....66 Volkhard Helms,J.Andrew McCammon Conformational Dynamics Simulations of Proteins.......... 78 Markus Eichinger,Berthold Heymann,Helmut Heller,Helmut Grubmiller,Paul Tavan Computation of Essential Molecular Dynamics by Subdivision Techniques 98 Peter Deuf lhard,Michael Dellnitz,Oliver Junge,Christof Schitte Mathematical Model of the Nucleic Acids Conformational Transitions with Hysteresis over Hydration-Dehydration Cycle..................116 Michael Ye.Tolstorukov,Konstantin M.Virnik II Thermodynamic Modelling Simulation Studies of Protein-Ligand Interactions...................129 Jan Hermans,Geoffrey Mann,Lu Wang,Li Zhang Estimating Relative Free Energies from a Single Simulation of the Ini- tial State................ Alan E.Mark,Heiko Schafer,Haiyan Liu,Wilfred van Gunsteren Exploration of Peptide Free Energy Surfaces......... 163 Krzysztof Kuczera Prediction of pKas of Titratable Residues in Proteins Using a Poisson- Boltzmann Model of the Solute-Solvent System.....................176
X Table of Contents Jan Antosiewicz,Elibieta Btachut-Okrasinska,Tomasz Grycuk, James M.Briggs,Stanistaw T.Wtodek,Bogdan Lesyng,J.Andrew McCammon Exploiting Tsallis Statistics... 197 John E.Straub,Joan Andricioaei New Techniques for the Construction of Residue Potentials for Protein Folding.………· …212 Arnold Neumaier,Stefan Dallwig,Waltraud Huyer,Hermann Schichl III Enhanced Time-Stepping Algorithms Some Failures and Successes of Long-Timestep Approaches to Biomolecular Simulations........................................227 Tamar Schlick Application of a Stochastic Path Integral Approach to the Computa- tions of an Optimal Path and Ensembles of Trajectories.............263 Ron Elber,Benoit Roux,Roberto Olender On Some Difficulties in Integrating Highly Oscillatory Hamiltonian Sys- tems..........................................................281 Uri M.Ascher,Sebastian Reich Molecular Dynamics in Systems with Multiple Time Scales:Reference System Propagator Algorithms........... 297 Bruce J.Berne The Five Femtosecond Time Step Barrier ......... :.,318 Robert D.Skeel,Jesis A.Izaguirre Long Time Step MD Simulations Using Split Integration Symplectic Method.……332 Dusanka Janezic,Franci Merzel Comparison of Geometric Integrators for Rigid Body Simulation......349 Benedict J.Leimkuhler IV Quantum-Classical Simulations New Methods in Quantum Molecular Dynamics of Large Polyatomic Systems.........365 Pavel Jungwirth,R.Benny Gerber
Table of Contents XI Approximation Properties and Limits of the Quantum-Classical Molec- ular Dynamics Model............................................ 380 Christof Schiitte,Folkmar A.Bornemann Numerical Integrators for Quantum-Classical Molecular Dynamics.....396 Peter Nettesheim,Christof Schitte Symplectic Multiple-Time-Stepping Integrators for Quantum-Classical Molecular Dynamics.............................................412 Peter Nettesheim,Sebastian Reich A Bunch of Time Integrators for Quantum/Classical Molecular Dynamics421 Marlis Hochbruck,Christian Lubich Applications of Ab-Initio Molecular Dynamics Simulations in Chem- istry and Polymer Science........................................433 Robert J.Meier Polarons of Molecular Crystal Model by Nonlocal Dynamical Coherent Potential Method...............................................442 Sergiy V.Izvekov V Parallel Force Field Evaluation Ewald and Multipole Methods for Periodic N-Body Problems .......459 John A.Board,Jr.,Christopher W.Humphres,Christophe G. Lambert,William T.Rankin,Abdulnour Y.Toukmaji Avoiding Algorithmic Obfuscation in a Message-Driven Parallel MD C0de...........................,,..。472 James C.Phillips,Robert Brunner,Aritomo Shinozaki, Milind Bhandarkar,Neal Krawetz,Attila Gursoy,Laxmikant Kale, Robert D.Skeel,Klaus Schulten Parallel Molecular Dynamics Using Force Decomposition.............483 Daniel Okunbor,Ravi Murty
Introductory Survey