## Computer simulation of biomolecular systems: theoretical and experimental applicationsThe long-range goal of molecular approaches to biology is to describe living systems in terms of chemistry and physics. Over the last fifty years great progress has been made in applying the equations representing the underlying physical laws to chemical problems involving the structures and reactions of small molecules. Corresponding studies of mesoscopic systems have been undertaken much more recently. Molecular dynamics simulations, which are the primary focus of this volume, represent the most important theoretical approach to macromolecules of biological interest. Now that molecular dynamics of macromolecules is a flourishing field, serious questions have to be asked concerning what more can be done with the methodology. What is the present and the future role of molecular dynamics in the development of our knowledge of macromolecules of biological interest? How does the methodology need to be improved to make it applicable to important problems? The present volume is concerned with providing some answers with its primary focus on the methodology and its recent developments. |

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### Contents

A primer | 3 |

Treatment of boundaries | 15 |

Integration schemes for MD and SD | 21 |

Copyright | |

79 other sections not shown

### Common terms and phrases

algorithm applications approach approximation atoms Berendsen bilayer Biol Biomolecular Systems boundary calculations CBMC chain charge Chem chemical potential Computer Simulation configuration conformation constant constraints contribution correlation cutoff defined degrees of freedom density derived determined dielectric dihedral angle dipoles distance distribution dynamics simulations effects electronic electrostatic energy function ensemble average evaluated experimental factor force field free energy difference geometry Gunsteren Hamiltonian hydrogen bonds implicit solvent integration interactions Karplus long-range matrix McCammon MD simulations method minimization molecular dynamics molecules Monte Carlo non-bonded number of particles obtained parameters partition function peptide Pettitt phase space Phys potential energy problem procedure protein protons range reaction coordinate reaction field refinement regions relaxation residues sampling scheme Scheraga simulated annealing solution solvation solvent statistical step structure surface techniques temperature thermodynamic tion torsion trajectories trial move truncation variables vector volume