Computational molecular dynamics: challenges, methods, ideas. Proceedings of the 2nd international symposium on Algorithms for Macromolecular modelling, Berlin, Germany, May 21--24, 1997 (Q1274146)

The articles of this volume will be reviewed individually. Indexed articles: \textit{Berendsen, Herman J. C.}, Molecular dynamics simulations: The limits and beyond, 3-36 [Zbl 0966.81068] \textit{Izrailev, Sergei; Stepaniants, Sergey; Isralewitz, Barry; Kosztin, Dorina; Lu, Hui; Molnar, Ferenc; Wriggers, Willy; Schulten, Klaus}, Steered molecular dynamics, 39-65 [Zbl 0965.92005] \textit{Helms, Volkhard; McCammon, J. Andrew}, Conformational transitions of proteins from atomistic simulations, 66-77 [Zbl 0964.92016] \textit{Eichinger, Markus; Heymann, Berthold; Heller, Helmut; Grubmüller, Helmut; Tavan, Paul}, Conformational dynamics simulations of proteins, 78-97 [Zbl 0964.92015] \textit{Deuflhard, Peter; Dellnitz, Michael; Junge, Oliver; Schütte, Christof}, Computation of essential molecular dynamics by subdivision techniques, 98-115 [Zbl 0966.81067] \textit{Tolstorukov, Michael Ye.; Virnik, Konstantin M.}, Mathematical model of the nucleic acids conformational transitions with hysteresis over hydration-dehidration cycle, 116-126 [Zbl 0964.92019] \textit{Hermans, Jan; Mann, Geoffrey; Wang, Lu; Zhang, Li}, Simulation studies of protein-ligand interactions, 129-148 [Zbl 0964.92017] \textit{Mark, Alan E.; Schäfer, Heiko; Liu, Haiyan; van Gunsteren, Wilfred}, Estimating relative free energies from a single simulation of the initial state, 149-162 [Zbl 0983.70016] \textit{Kuczera, Krysztof}, Exploration of peptide free energy surfaces, 163-175 [Zbl 1002.92529] \textit{Antosiewicz, Jan; Blachut-Okrasińska, Elżbieta; Grycuk, Tomasz; Briggs, James M.; Włodek, Stanisław T.; Lesyng, Bogdan; McCammon, J. Andrew}, Prediction of pK\(_a\)s of titratable residues in proteins using a Poisson-Boltzmann model of the solute-solvent system, 176-196 [Zbl 0965.92004] \textit{Straub, John E.; Andricioaei, Ioan}, Exploiting Tsallis statistics., 197-211 [Zbl 1043.82505] \textit{Neumaier, Arnold; Dallwig, Stefan; Huyer, Waltraud; Schichl, Hermann}, New techniques for the construction of residue potentials for protein folding, 212-224 [Zbl 0965.92021] \textit{Schlick, Tamar}, Some failures and successes of long-timestep approaches to biomolecular simulations, 227-262 [Zbl 0964.92018] \textit{Elber, Ron; Roux, Benoit; Olender, Roberto}, Application of a stochastic path integral approach to the computations of an optimal path and ensembles of trajectories, 263-280 [Zbl 0966.81038] \textit{Ascher, Uri M.; Reich, Sebastian}, On some difficulties in integrating highly oscillatory Hamiltonian systems, 281-296 [Zbl 0971.65113] \textit{Berne, Bruce J.}, Molecular dynamics in systems with multiple time scales: reference system propagator algo\-rithms., 297-317 [Zbl 1043.82541] \textit{Skeel, Robert D.; Izaguirre, Jesús A.}, The five femtosecond time step barrier, 318-331 [Zbl 1002.92530] \textit{Janežič, Dušanka; Merzel, Franci}, Long time step MD simulations using split integration symplectic method, 332-348 [Zbl 0966.81065] \textit{Leimkuhler, Benedict J.}, Comparison of geometric integrators for rigid body simulation, 349-362 [Zbl 0982.70002] \textit{Jungwirth, Pavel; Gerber, R. Benny}, New methods in quantum molecular dynamics of large polyatomic systems, 365-379 [Zbl 0966.81062] \textit{Schütte, Christof; Bornemann, Folkmar A.}, Approximation properties and limits of the quantum-classical molecular dynamics model, 380-395 [Zbl 0966.81063] \textit{Nettesheim, Peter; Schütte, Christof}, Numerical integrators for quantum-classical molecular dynamics, 396-411 [Zbl 0966.81064] \textit{Nettesheim, Peter; Reich, Sebastian}, Symplectic multiple-time-stepping integrators for quantum-classical molecular dynamics, 412-420 [Zbl 0970.81104] \textit{Hochbruk, Marlis; Lubich, Christian}, A bunch of time integrators for quantum/classical molecular dynamics, 421-432 [Zbl 0966.81066] \textit{Meier, Robert J.}, Applications of ab-initio molecular dynamics simulations in chemistry and polymer science., 433-441 [Zbl 1043.82502] \textit{Izvekov, Sergiy V.}, Polarons of molecular crystal model by nonlocal dynamical coherent potential method., 442-456 [Zbl 1043.82501] \textit{Board, John A. jun.; Humphres, Christopher W.; Lambert, Christophe G.; Rankin, William T.; Toukmaji, Abdulnour Y.}, Ewald and multipole methods for periodic \(N\)-body problems., 459-471 [Zbl 1043.81502] \textit{Phillips, James C.; Brunner, Robert; Shinozaki, Aritomo; Bhandakar, Milind; Kraewetz, Neal; Gursoy, Attila; Kalé, Laxmikant; Skeel, Robert D.; Schulten, Klaus}, Avoiding algorithmic obfuscation in a message-driven parallel MD code, 472-482 [Zbl 0966.81060] \textit{Okunbor, Daniel; Murty, Ravi}, Parallel molecular dynamics using force decomposition., 483-494 [Zbl 1043.81504]