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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: Introduction Laboratory and computer experiment, methods molecular dynamics (MD) and Monte Carlo (MC). Description of many particle system, intermolecular forces, correlation functions. Basics of MC Mathematical formulation of the problem, naive and preferential sampling, lattice systems, simulations in NPT and NVT ensembles, boundary conditions and technical details, optimization. Applications: hard sphere and Lennard-Jones liquids Basics of MD Equations of motion, Verlet and Gear integrators, simple thermostats. Applications: particles in homogeneous and radial gravitation fields, Lennard-Jones liquid. 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)
- Class attendance
- 39 hours per semester
- Preparation for classes
- 39 hours per semester
- Preparation for exam
- 40 hours per semester
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Learning outcomes
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Introduce students to non-quantum computer simulations in molecular physics - molecular dynamics, Monte Carlo. Solving practical tasks in GROMACS, LAMMPS. Learn the style of work in computer modelling by using computer pseudo-experiments. Learn to work in a supercomputer environment (Metacenter).
Student will understand simulations as a computer (pseudo)experiment, will be able to prepare, run, and analyze molecular simulations in programs Gromacs a LAMMPS.
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Prerequisites
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Basics of work in linux (can be quickly gained).
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Assessment methods and criteria
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Oral examination, Student performance assessment, Analysis of student's work activities (technical works)
Criteria for obtaining the course credit (zápočet): Solving at least 70% of tasks solved during exercises with the help of the teacher. Independent solution of individual tasks to at least 50%. Criterium for passing the exam: At least 50% knowledge of the topic contained in the two drawn questions.
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Recommended literature
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D. Frenkel, B. Smit, Understanding Molecular Simulation, Academic Press, 2002..
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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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Uživatelský manuál a návody (tutorials) k programu GROMACS: http://www.gromacs.org.
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