## Computational molecular dynamics: challenges, methods, ideas : proceedings of the 2nd International Symposium on Algorithms for Macromolecular Modelling, Berlin, May 21-24, 1997On 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. |

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### Contents

The Limits and Beyond | 3 |

Steered Molecular Dynamics | 39 |

Conformational Transitions of Proteins from Atomistic Simulations | 66 |

Copyright | |

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### Common terms and phrases

accuracy acid algorithm analysis applications approach approximation atoms average Berendsen biomolecular bond BPTI calculations Chem classical Comp complex components computed configurations conformational transitions conserving constant coordinates corresponding degrees of freedom density described discretization distribution efficient eigenvalues electrostatic equations of motion equilibrium error estimate evaluation exciton force field free energy function Gunsteren Hamiltonian systems harmonic hydrogen bonds initial interactions invariant ionization kcal/mol Langevin Langevin dynamics ligand linear matrix McCammon MD simulations mechanics molecular dynamics molecular dynamics simulations Monte Carlo NAMD numerical integrators obtained optimization oscillations parallel particles peptide perturbation phase space phonon Phys potential energy problem processors propagator properties protein protein folding proton QCMD quantum quantum-classical reaction residues rigid body sampling scheme Schlick Schulten SISM Skeel solution solvent stability step stepsize structure symplectic integrators techniques thermodynamic timestep tion trajectory unbinding vector velocity Verlet Verlet integrator water molecules