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Molecular Dynamics
F3 2016 . 2017 - 1º semestre
syllabus and bibliography Statistical mechanics review: ensembles, fluctuations, correlation functions and transport coefficients.
Empirical and semi-empirical pair- and inter-molecular potentials. Classical molecular dynamics: equations of motion, simulation initialisation, algorithms for integration of the equations of motion, Liouville formulation. Simulations at constant temperature or pressure: Andersen and Nosé-Hoover thermostats and barostats. Free-energy calculations: thermodynamic integration, chemical potential, Gibbs ensemble, free energies of solids, non equilibrium systems. Technical details: long-range interactions, rare events, supercomputers. Ab-initio molecular dynamics: Born-Oppenheimer, Ehrenfest, Car-Parrinello, QM/MM. Applications. Bibliography of reference Understanding Molecular Simulation: From Algorithms to Applications
Daan Frenkel and Berend Smit Academic Press (2002) Computer Simulation of Liquids M. P. Allen and D. J. Tildesley Oxford University Press (1987) Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods Dominik Marx and Jürg Hutter Cambridge University Press (2009) The Art of Molecular Dynamics Simulation D. C. Rapaport Cambridge University Press (2004) A molecular dynamics primer Furio Ercolessi http://www.fisica.uniud.it/~ercolessi/md/md/ Molecular dynamics without effective potentials via the Car-Parrinello approach Dahlia K. Remler , Paul A. Madden Molecular Physics 70 (1990) 921-966 Iterative minimization techniques for ab initio total-energy calculations: molecular dynamics and conjugate gradients M. C. Payne, M. P. Teter, D. C. Allan, T. A. Arias, and J. D. Joannopoulos Rev. Mod. Phys. 64 (1992) 1045-1097
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