Title | Computational Molecular Dynamics: Challenges, Methods, Ideas [electronic resource] : Proceedings of the 2nd International Symposium on Algorithms for Macromolecular Modelling, Berlin, May 21-24, 1997 / edited by Peter Deuflhard, Jan Hermans, Benedict Leimkuhler, Alan E. Mark, Sebastian Reich, Robert D. Skeel |
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Imprint | Berlin, Heidelberg : Springer Berlin Heidelberg : Imprint: Springer, 1999 |
Connect to | http://dx.doi.org/10.1007/978-3-642-58360-5 |
Descript | XI, 494 p. online resource |
Introductory Survey -- Molecular Dynamics Simulations: The Limits and Beyond -- I Conformational Dynamics -- Steered Molecular Dynamics -- Conformational Transitions of Proteins from Atomistic Simulations -- Conformational Dynamics Simulations of Proteins -- Computation of Essential Molecular Dynamics by Subdivision Techniques -- Mathematical Model of the Nucleic Acids Conformational Transitions with Hysteresis over Hydration-Dehydration Cycle -- II Thermodynamic Modelling -- Simulation Studies of Protein-Ligand Interactions -- Estimating Relative Free Energies from a Single Simulation of the Initial State -- Exploration of Peptide Free Energy Surfaces -- Prediction of pKas of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute-Solvent System -- Exploiting Tsallis Statistics -- New Techniques for the Construction of Residue Potentials for Protein Folding -- III Enhanced Time-Stepping Algorithms -- Some Failures and Successes of Long-Timestep Approaches to Biomolecular Simulations -- Application of a Stochastic Path Integral Approach to the Computations of an Optimal Path and Ensembles of Trajectories -- On Some Difficulties in Integrating Highly Oscillatory Hamiltonian Systems -- Molecular Dynamics in Systems with Multiple Time Scales: Reference System Propagator Algorithms -- The Five Femtosecond Time Step Barrier -- Long Time Step MD Simulations Using Split Integration Symplectic Method -- Comparison of Geometric Integrators for Rigid Body Simulation -- IV Quantum-Classical Simulations -- New Methods in Quantum Molecular Dynamics of Large Polyatomic Systems -- Approximation Properties and Limits of the Quantum-Classical Molecular Dynamics Model -- Numerical Integrators for Quantum-Classical Molecular Dynamics -- Symplectic Multiple-Time-Stepping Integrators for Quantum-Classical Molecular Dynamics -- A Bunch of Time Integrators for Quantum/Classical Molecular Dynamics -- Applications of Ab-Initio Molecular Dynamics Simulations in Chemistry and Polymer Science -- Polarons of Molecular Crystal Model by Nonlocal Dynamical Coherent Potential Method -- V Parallel Force Field Evaluation -- Ewald and Multipole Methods for PeriodicN-Body Problems -- Avoiding Algorithmic Obfuscation in a Message-Driven Parallel MD Code -- Parallel Molecular Dynamics Using Force Decomposition