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Download Computational Molecular Dynamics: Challenges, Methods, by Herman J. C. Berendsen (auth.), Peter Deuflhard, Jan PDF

By Herman J. C. Berendsen (auth.), Peter Deuflhard, Jan Hermans, Benedict Leimkuhler, Alan E. Mark, Sebastian Reich, Robert D. Skeel (eds.)

On may perhaps 21-24, 1997 the second one overseas Symposium on Algorithms for Macromolecular Modelling used to be held on the Konrad Zuse Zentrum in Berlin. the development introduced jointly computational scientists in fields like biochemistry, biophysics, actual chemistry, or statistical physics and numerical analysts in addition to laptop scientists engaged on the development of algorithms, for a complete of over one hundred twenty individuals from 19 international locations. throughout the symposium, the audio system agreed to supply a consultant quantity that mixes survey articles and unique papers (all refereed) to provide an influence of the current state-of-the-art of Molecular Dynamics.
The 29 articles of the e-book mirror the most themes of the Berlin assembly that have been i) Conformational Dynamics, ii) Thermodynamic Modelling, iii) complex Time-Stepping Algorithms, iv) Quantum-Classical Simulations and speedy strength box and v) speedy strength box Evaluation.

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Extra info for Computational Molecular Dynamics: Challenges, Methods, Ideas: Proceedings of the 2nd International Symposium on Algorithms for Macromolecular Modelling, Berlin, May 21–24, 1997

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I. Theory. J. Chern. Phys. 104 (1996) 2018-2027. 126. : Adiabatic path integral molecular dynamics methods. II. Algorithms. J. Chern. Phys. 104 (1996) 2028-2035. 127. : A path integral study of electronic polarization and nonlinear coupling effects in condensed phase proton transfer reactions. Chem. Phys. 100 (1994) 3039-3047. 128. : The quantum dynamics of an excess proton in water. Chem. Phys. 104 (1996) 2056-2069. 129. : Determination of proton transfer rate constants using ab initio, molecular dynamics and density matrix evolution calculations.

Chem. Phys. 104 (1996) 2056-2069. 129. : Determination of proton transfer rate constants using ab initio, molecular dynamics and density matrix evolution calculations. Pacific Symposium on Biocomputing, World Scientific, Singapore (1996) 1-14. 130. : The rate of proton transfer in the active site of HIV-1 protease. Submitted, 1998. 131. : Simulation of a slow reaction with quantum character: Neutral hydrolysis of a carboxylic ester. Submitted (1998). 132. : Simulation of water transport through a lipid membrane.

Besides yielding qualitative information, these biologically and pharmaceutically motivated applications of SMD can also yield quantitative information about the binding potential of the ligand-receptor complex. A first advance in the reconstruction of the thermodynamic potential from SMD data by discounting irreversible work was made by Balsera et al. (1997) as outlined in Sect. "Reconstruction of the potential of mean force" below. In the following we describe the methodology of SMD, illustrate applications of SMD through key examples, present the non-equilibrium statistical mechanical theory of SMD, and describe a method of reconstruction of a potential of mean force from SMD data.

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