Computational Molecular Dynamics Challenges Methods Ideas by Peter Deuflhard, Jan Hermans, Benedict Leimkuhler, Alan E. PDF

By Peter Deuflhard, Jan Hermans, Benedict Leimkuhler, Alan E. Mark, Sebastian Reich, Robert D. Skeel

ISBN-10: 3540632425

ISBN-13: 9783540632429

On could 21-24, 1997 the second one foreign 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 a hundred and twenty individuals from 19 nations. during the symposium, the audio system agreed to provide 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 ebook replicate the most themes of the Berlin assembly which have been i) Conformational Dynamics, ii) Thermodynamic Modelling, iii) complex Time-Stepping Algorithms, iv) Quantum-Classical Simulations and quickly strength box and v) speedy strength box review.

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Chem. Phys. 101 (1994) 734-748. 75. : NAMD - A parallel, object-oriented molecular dynamics program. Int. J. Supercomputing Applications and High Performance Computing 10 (1996) 251-268. 76. Esselink, K. : A comparison of algorithms for long-range interactions. Comput. Phys. Comm. 87 (1995) 375-395. 77. : A comparison of particle-particle particle-mesh and Ewald methods for calculating interactions in periodic molecular systems. Mol. Simul. 14 (1994) 11-20. 78. : Molecular dynamics simulations of water with Ewald summation for the long-range electrostatic interactions.

Comput. Theor. Polymer Sci. 6 (1996) 1-8. 148. M. : Mesoscopic dynamics of copolymer melts: from density dynamics to external potential dynamics using nonlocal kinetic coupling. J. Chem. Phys. 107 (1997) 5879-5889. 149. Fraaije, J. : The dynamic mean-field density functional method and its application to the mesoscopic dynamics of quenched block copolymer melts. J. Chem. Phys. 106 (1997) 4260-4269. Part I Conformational Dynamics Steered Molecular Dynamics Sergei Izrailev, Sergey Stepaniants, Barry Isralewitz, Dorina Kosztin, Hui Lu, Ferenc Molnar, Willy Wriggers, and Klaus Schulten Beckman Institute, University of Illinois at Urbana-Champaign, 405 N.

The structure presents a snapshot of the SMD simulation with retinal (dark spheres) partially extracted from the protein bR through an opening between helices E and F into the hydrophobic phase of the surrounding membrane. (b) Magnification of boxed area in (a), a t completion of retinal's exit from bR, representing the putative exit/entry window of retinal. The amino acids shown, Ala144, Met 145, and Ser183, form a hydrogen bond network with retinal's carbonyl group attracting and guiding retinal into the protein.

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Computational Molecular Dynamics Challenges Methods Ideas by Peter Deuflhard, Jan Hermans, Benedict Leimkuhler, Alan E. Mark, Sebastian Reich, Robert D. Skeel


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