Methods for Macromolecular Modeling (M3): Assessment of Progress and Future Perspectives -- I Biomolecular Dynamics Applications -- Mathematics and Molecular Neurobiology -- Structural and Dynamical Characterization of Nuclei Acid Water and Ion Binding Sites -- II Molecular Dynamics Methods -- A Test Set for Molecular Dynamics Algorithms -- Internal Coordinate Molecular Dynamics Based on the Spectroscopic B-Matrix -- The Sigma MD Program and a Generic Interface Applicable to Multi-Functional Programs with Complex, Hierarchical Command Structure -- Overcoming Instabilities in Verlet-I/r-RESPA with the Mollified Impulse Method -- III Monte Carlo Methods -- On the Potential of Monte Carlo Methods for Simulating Macromolecular Assemblies -- Structure Calculation of Protein Segments Connecting Domains with Defined Secondary Structure: A Simulated Annealing Monte Carlo Combined with Biased Scaled Collective Variables Technique -- IV Other Conformational Sampling Methods -- Hierarchical Uncoupling-Coupling of Metastable Conformations -- Automatic Identification of Metastable Conformations via Self-Organized Neural Networks -- V Free Energy Methods -- Equilibrium and Non-Equilibrium Foundations of Free Energy Computational Methods -- Free-Energy Calculations in Protein Folding by Generahzed-Ensemble Algorithms -- Ab Initio QM/MM and Free Energy Calculations of Enzyme Reactions -- VI Long Range Interactions and Fast Electrostatics Methods -- Treecode Algorithms for Computing Nonbonded Particle Interactions -- A New Reciprocal Space Based Method for Treating Long Range Interactions in Ab Initio and Force-Field Based Calculations for Surfaces, Wires, and Clusters -- Efficient Computational Algorithms for Fast Electrostatics and Molecular Docking -- VII Statistical Approaches to Protein Structures -- Fold Recognition Using the OPLS All-Atom Potential and the Surface Generalized Born Solvent Model -- Identification of Sequence-Specific Tertiary Packing Motifs in Protein Structures using Delaunay Tessellation -- Appendix: Color Plates

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