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Last update: Kolafa Jiří prof. RNDr. CSc. (17.09.2015)
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Last update: Kolafa Jiří prof. RNDr. CSc. (17.09.2015)
Students will understand the principles of molecular modeling and simulation in the frame of quantum and classical thermodynamics. They will master MC and MD simulation methods including determination of various quantities. The students will be able to devise a computer experiment. |
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Last update: Kolafa Jiří prof. RNDr. CSc. (17.09.2015)
D. Frenkel a B. Smit: Understanding Molecular Simulation (Academic Press, 1996, 2002); M. P. Allen a D. J. Tildesley: Computer Simulation of Liquids (Clarendon Press, Oxford 1986, 2002); |
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Last update: Kolafa Jiří prof. RNDr. CSc. (17.09.2015)
http://old.vscht.cz/fch/en/tools/kolafa/S403027.html |
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Last update: Kolafa Jiří prof. RNDr. CSc. (11.04.2018)
1. Introduction - What are simulations good for? 2. Repetition of statistical thermodynamics and less common ensembles (isobaric). 3. Atomistic and lattice models. Force field. 4. Molecular dynamics: Verlet's method, leap-frog. Fundamentals of Hamilton's mechanics, conservation laws. Symplecticity. 5. Other integrators (Gear, multiple timestep). Thermostats in MD. 6. Monte Carlo Methods - MC integration, Metropolis method. Random numbers. 7. Methodology of simulations and measurement of quantities, statistical errors. Boundary conditions. 8. Structural quantities: radial distribution functions, structure factor. 9. Entropic quantities: thermodynamic integration, non-Boltzmann sampling, integration of mean force, Widom's method. 10. Potential range, cutoff corrections. Coulomb's forces: Ewald summation, reaction field. 11. Other ensembles: isobaric, grandkanonical, Gibbs. Additional degrees of freedom in MD: Nose-Hoover, barostat. 12. Other MC methods: preferential sampling, molecules, polymers. Constraint dynamics (SHAKE). Optimization of simulations. 13. Brownian (Langevin) dynamics and DPD. Kinetic quantities: EMD vs. NEMD. 14. Optimization: Simulated annealing, genetic algorithms. |
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Last update: Kolafa Jiří prof. RNDr. CSc. (17.09.2015)
Good knowledge of chemical and statistical thermodynamics, basic knowledge of theoretical mechanics |