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Last update: JUNGWIRT (29.05.2007)
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Last update: prof. RNDr. Marek Procházka, Ph.D. (14.05.2020)
Oral exam, exam requirements - in the extent of the syllabus. |
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Last update: prof. RNDr. Marek Procházka, Ph.D. (28.01.2019)
M. P. Allen a D. J. Tildesley: Computer simulations of liquids, Clarendon Press, Oxford, 1991. D. Frenkel a B. Smit: Understanding molecular simulations, Academic Press, New York, 2002. H. Martinez-Seara a L. Cwiklik; Introductory tutorial for Gromacs, DOI: 10.5281/zenodo.1230441 E. Braun et al., Best Practices for Foundations in Molecular Simulations, Living Journal of Computational Molecular Science 1.1 (2018): 5957.
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Last update: prof. RNDr. Marek Procházka, Ph.D. (14.05.2020)
Oral exam requirements are within the scope of the lecture syllabus. |
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Last update: JUNGWIRT (30.05.2007)
1. Minireview of statistical mechanics - thermodynamic ensembles, calculation of thermodynamic variables, correlation and distribution functions, ergodic theorem.
2. Interatomic and intermolecular potentials.
3. Integration of classical equations of motion - Verlet method, predictor-corrector (Gear) method.
4. Basics of Monte Carlo methods. Metropolis method of generation of the canonical ensemble.
5. Simulation protocole: initial conditions, entry parameters, periodic boundary conditions, interaction cutoff, Ewald summation, methods of temperature and pressure control.
6. Methods of visualization and analysis of results.
Within the class there will be both theoretical lectures and practical demonstrations of computer simulations. |