Computational Molecular Dynamics: Challenges, Methods, Ideas

1. Front Matter

   Pages N1-XI

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2. Introductory Survey

   1. Front Matter

      Pages 1-1

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   2. Molecular Dynamics Simulations: The Limits and Beyond

      • Herman J. C. Berendsen

      Pages 3-36

3. Conformational Dynamics

   1. Front Matter

      Pages 37-37

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   2. Steered Molecular Dynamics

      • Sergei Izrailev, Sergey Stepaniants, Barry Isralewitz, Dorina Kosztin, Hui Lu, Ferenc Molnar et al.

      Pages 39-65

   3. Conformational Transitions of Proteins from Atomistic Simulations

      • Volkhard Helms, J. Andrew McCammon

      Pages 66-77

   4. Conformational Dynamics Simulations of Proteins

      • Markus Eichinger, Berthold Heymann, Helmut Heller, Helmut Grubmüller, Paul Tavan

      Pages 78-97

   5. Computation of Essential Molecular Dynamics by Subdivision Techniques

      • Peter Deuflhard, Michael Dellnitz, Oliver Junge, Christof Schütte

      Pages 98-115

   6. Mathematical Model of the Nucleic Acids Conformational Transitions with Hysteresis over Hydration—Dehydration Cycle

      • Michael Ye. Tolstorukov, Konstantin M. Virnik

      Pages 116-126

4. Thermodynamic Modelling

   1. Front Matter

      Pages 127-127

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   2. Simulation Studies of Protein-Ligand Interactions

      • Jan Hermans, Geoffrey Mann, Lu Wang, Li Zhang

      Pages 129-148

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

      • Alan E. Mark, Heiko Schäfer, Haiyan Liu, Wilfred van Gunsteren

      Pages 149-162

   4. Exploration of Peptide Free Energy Surfaces

      • Krzysztof Kuczera

      Pages 163-175

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

      • Jan Antosiewicz, Elzbieta Błachut-Okrasińska, Tomasz Grycuk, James M. Briggs, Stanisław T. Włodek, Bogdan Lesyng et al.

      Pages 176-196

   6. Exploiting Tsallis Statistics

      • John E. Straub, Ioan Andricioaei

      Pages 197-211

   7. New Techniques for the Construction of Residue Potentials for Protein Folding

      • Arnold Neumaier, Stefan Dallwig, Waltraud Huyer, Hermann Schichl

      Pages 212-224

5. Enhanced Time-Stepping Algorithms

   1. Front Matter

      Pages 225-225

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

      • Tamar Schlick

      Pages 227-262

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

      • Ron Elber, Benoit Roux, Roberto Olender

      Pages 263-280

   4. On Some Difficulties in Integrating Highly Oscillatory Hamiltonian Systems

      • Uri M. Ascher, Sebastian Reich

      Pages 281-296

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.

• Approximation
• Potential
• Radiologieinformationssystem
• algorithms
• statistics

• Konrad-Zuse-Zentrum Berlin (ZIB), Berlin-Dahlem, Germany

  Peter Deuflhard

• Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, USA

  Jan Hermans

• Department of Mathematics, University of Kansas, Lawrence, USA

  Benedict Leimkuhler

• Laboratorium für Physikalische Chemie ETH Zentrum, Zürich, Switzerland

  Alan E. Mark

• Department of Mathematics and Statistics, University of Surrey, Guildford, Surrey, UK

  Sebastian Reich

• Department of Computer Science, University of Illinois, Urbana, USA

  Robert D. Skeel

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