Introductory Survey

Molecular Dynamics Simulations: The Limits and Beyond

Herman J. C. Berendsen

I Conformational Dynamics

Steered Molecular Dynamics

Sergei Izrailev

Sergey Stepaniants

Barry Isralewitz

Dorina Kosztin

Hui Lu

Ferenc Molnar

Willy Wriggers

Klaus Schulten

Conformational Transitions of Proteins from Atomistic Simulations

Volkhard Helms

J. Andrew McCommon

Conformational Dynamics Simulations of Proteins

Markus Eichinger

Berthold Heymann

Helmut Heller

Helmut Grubmuller

Paul Tavan

Computation of Essential Molecular Dynamics by Subdivision Techniques

Peter Deuf lhard

Michael Dellnitz

Oliver Junge

Christof Schutte

Mathematical Model of the Nucleic Acids Conformational Transitions with Hysteresis over Hydration--Dehydration Cycle

Michael Ye. Tolstorukov

Konstantin M. Virnik

II Thermodynamic Modelling

Simulation Studies of Protein-Ligand Interactions

Jan Hermans

Geoffrey Mann

Lu Wang

Li Zhang

Estimating Relative Free Energies from a Single Simulation of the Initial State

Alan E. Mark

Heiko Schafer

Haiyan Liu

Wilfred van Gunsteren

Exploration of Peptide Free Energy Surfaces

Krzysztof Kuczera

Prediction of pKas of Titratable Residues in Proteins Using a Poisson- Boltzmann Model of the Solute-Solvent System

Jan Antosiewicz

Elzbieta Blachut-Okrasinska

Tomasz Grycuk

James M. Briggs

Stanislaw T. Wlodek

Bogdan Lesyng

J. Andrew McCammon

Exploiting Tsallis Statistics

John E. Straub

Ioan Andricioaei

New Techniques for the Construction of Residue Potentials for Protein Folding

Arnold Neumaier

Stefan Dallwig

Waltraud Huyer

Hermann Schichl

III Enhanced Time-Stepping Algorithms

Some Failures and Successes of Long-Timestep Approaches to Biomolecular Simulations

Tamar Schlick

Application of a Stochastic Path Integral Approach to the Computations of an Optimal Path and Ensembles of Trajectories

Ron Elber

Benoit Roux

Roberto Olender

On Some Difficulties in Integrating Highly Oscillatory Hamiltonian Systems

Uri M. Ascher

Sebastian Reich

Molecular Dynamics in Systems with Multiple Time Scales: Reference System Propagator Algorithms

Bruce J. Berne

The Five Femtosecond Time Step Barrier

Robert D. Skeel

Jesus A. Izaguirre

Long Time Step MD Simulations Using Split Integration Symplectic Method

Dusanka Janezic

Franci Merzel

Comparison of Geometric Integrators for Rigid Body Simulation

Benedict J. Leimkuhler

IV Quantum-Classical Simulations

New Methods in Quantum Molecular Dynamics of Large Polyatomic Systems

Pavel Jungwirth

R. Benny Gerber

Approximation Properties and Limits of the Quantum-Classical Molecular Dynamics Model

Christof Schutte

Folkmar A. Bornemann

Numerical Integrators for Quantum-Classical Molecular Dynamics

Peter Nettesheim

Christof Schutte

Symplectic Multiple-Time-Stepping Integrators for Quantum-Classical Molecular Dynamics

Peter Nettesheim

Sebastian Reich

A Bunch of Time Integrators for Quantum / Classical Molecular Dynamics

Marlis Hochbruck

Christian Lubich

Applications of Ab-Initio Molecular Dynamics Simulations in Chemistry and Polymer Science

Robert J. Meier

Polarons of Molecular Crystal Model by Nonlocal Dynamical Coherent Potential Method

Sergiy V. Izvekov

V Parallel Force Field Evaluation

Ewald and Multipole Methods for Periodic N-Body Problems

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 Code

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