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Lecturer(s)
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Předota Milan, doc. RNDr. Ph.D.
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Course content
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Content of lectures: Advanced techniques Non-Boltzmann sampling of configurational space, Nosé thermostat in MD. Simulations of charged and molecular systems Reaction field method and Ewald summation, simulations of rigid molecules, simulations of molecules with internal degrees of freedom, dynamics with constraints. Phase transitions and critical phenomena Calculation of entropic properties, measurement of chemical potential, thermodynamics integration method, Gibbs ensemble, determination of phase equilibria, determination of critical temperature. Nonequilibrium systems close to equilibrium Methodology of simulations of nonequilibrium effects, kinetic coefficients, time correlation functions, Einstein's formula, nonequilibrium MD, kinetic MC - choice of kinetics, time in kinetic MC Content of practicals: Solving of simulation tasks in accord with the content of the lectures.
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Learning activities and teaching methods
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Monologic (reading, lecture, briefing), Demonstration, Activating (simulations, games, drama)
- Preparation for classes
- 10 hours per semester
- Preparation for exam
- 10 hours per semester
- Class attendance
- 28 hours per semester
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Learning outcomes
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Advanced Monte Carlo and molecular dynamics methods, applications to charged and molecular systems, nonequilibrium systems, determination of phase equilibria.
Theoretical basics of advanced simulation techniques, ability to perform non-equilibrium simulations in software Gromacs
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Prerequisites
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Completion of either course UFY/SIM1 or UFY/PFM
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Assessment methods and criteria
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Oral examination, Student performance assessment
To acquaint students with advanced molecular dynamics and methods for efficient sampling (metadynamics, potential of mean force calculations), non-equilibrium simulations.
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Recommended literature
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D. Frenkel, B. Smit, Understanding Molecular Simulation.
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I. Nezbeda, J. Kolafa, M. Kotrla, Úvod do počítačových simulací: Metody Monte Carlo a molekuární dynamiky, Karolinum 2003..
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