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Course, academic year 2022/2023
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Molecular Dynamics and Monte Carlo Methods - NBCM051
Title: Metody molekulové dynamiky a Monte Carlo
Guaranteed by: Department of Chemical Physics and Optics (32-KCHFO)
Faculty: Faculty of Mathematics and Physics
Actual: from 2020
Semester: winter
E-Credits: 5
Hours per week, examination: winter s.:2/1, C+Ex [HT]
Capacity: unlimited
Min. number of students: unlimited
Virtual mobility / capacity: no
State of the course: taught
Language: Czech
Teaching methods: full-time
Guarantor: prof. Dr. habil. Lukasz Cwiklik, Ph.D.
prof. Mgr. Pavel Jungwirth, CSc., DSc.
Class: Fyzika
Classification: Physics > Biophysics and Chemical Physics
Annotation -
Last update: JUNGWIRT (29.05.2007)
Introduction to molecular dynamics and Monte Carlo methods for simulating molecular systems. Suitable primarily for Ms. and PhD. students at MFF UK and PrF UK.
Course completion requirements -
Last update: prof. RNDr. Marek Procházka, Ph.D. (14.05.2020)

Oral exam, exam requirements - in the extent of the syllabus.

Literature - Czech
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.

Requirements to the exam -
Last update: prof. RNDr. Marek Procházka, Ph.D. (14.05.2020)

Oral exam requirements are within the scope of the lecture syllabus.

Syllabus -
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.

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