Molecular Dynamics Simulations

Kurt Binder (Institute of Physics Mainz), Jurgen Horbach (Institute of Physics Mainz), Walter Kob (Laboratoire des Verres Montpellier), Wolfgang Paul (Institute of Physics Mainz), Fathollah Varnik (CECAM Lyon)

Abstract: A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is discussed, and the basic MD algorithms are described. The sampling of intensive variables (temperature T, pressure p) in runs carried out in the microcanonical (NVE) ensemble (N= particle number, V = volume, E = energy) is discussed, as well as the realization of other ensembles (e.g. the NVT ensemble). For a typical application example, molten SiO2, the estimation of various transport coefficients (self-diffusion constants, viscosity, thermal conductivity) is discussed. As an example of Non-Equilibrium Molecular Dynamics (NEMD), a study of a glass-forming polymer melt under shear is mentioned.

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* Vol. 35 Dreistufig parallele Software zur Parameteroptimierung von Support-Vektor-Maschinen mit kostensensitiven Gütemaßen
Tatjana Eitrich
ISBN 978-3-9810843-1-3, March 2007, 262 pages, PDF
* Vol. 34 From Computational Biophysics to Systems Biology 2006
Proceedings
U.E.H. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.)
ISBN-10 3-9810843-0-6, ISBN-13 978-3-9810843-0-6, September 2006, 224 pages, PDF
* Vol. 33 Parallel Computing: Current & Future Issues of High-End Computing
Proceedings of the International Conference ParCo 2005
G.R. Joubert, W.E. Nagel, F.J. Peters,
O. Plata, P. Tirado, E. Zapata (Editors)
ISBN 3-00-017352-8, October 2006, 930 pages, PDF (57 MB)
* Vol. 32 NIC Symposium 2006
Proceedings
G. Münster, D. Wolf, M. Kremer (Editors)
Symposium, 1 – 2 March 2006, Forschungszentrum Jülich
ISBN 3-00-017351-X, February 2006, 384 pages
* Vol. 31 Computational Nanoscience: Do It Yourself!
Lecture Notes
Johannes Grotendorst, Stefan Blügel, Dominik Marx (Editors)
Winter School, 14. – 22 February 2006, Forschungszentrum Jülich
ISBN 3-00-017350-1, February 2006, 528 pages