Table of Contents Introductory Survey Molecular Dynamics Simulations:The Limits and Beyond............ 3 Herman J.C.Berendsen Conformational Dynamics Steered Molecular Dynamics...................................... 39 Sergei Izrailev,Sergey Stepaniants,Barry Isralewitz,Dorina Kosztin,Hui Lu,Ferenc Molnar,Willy Wriggers,Klaus Schulten Conformational Transitions of Proteins from Atomistic Simulations....66 Volkhard Helms,J.Andrew McCammon Conformational Dynamics Simulations of Proteins.......... 78 Markus Eichinger,Berthold Heymann,Helmut Heller,Helmut Grubmiller,Paul Tavan Computation of Essential Molecular Dynamics by Subdivision Techniques 98 Peter Deuf lhard,Michael Dellnitz,Oliver Junge,Christof Schitte Mathematical Model of the Nucleic Acids Conformational Transitions with Hysteresis over Hydration-Dehydration Cycle..................116 Michael Ye.Tolstorukov,Konstantin M.Virnik II Thermodynamic Modelling Simulation Studies of Protein-Ligand Interactions...................129 Jan Hermans,Geoffrey Mann,Lu Wang,Li Zhang Estimating Relative Free Energies from a Single Simulation of the Ini- tial State................ Alan E.Mark,Heiko Schafer,Haiyan Liu,Wilfred van Gunsteren Exploration of Peptide Free Energy Surfaces......... 163 Krzysztof Kuczera Prediction of pKas of Titratable Residues in Proteins Using a Poisson- Boltzmann Model of the Solute-Solvent System.....................176