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Course, academic year 2023/2024
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Methods of molecular dynamics and Monte Carlo - MC260P79
Title: Metody molekulové dynamiky a Monte Carlo
Czech title: Metody molekulové dynamiky a Monte Carlo
Guaranteed by: Department of Physical and Macromolecular Chemistry (31-260)
Faculty: Faculty of Science
Actual: from 2016
Semester: winter
E-Credits: 4
Examination process: winter s.:
Hours per week, examination: winter s.:2/1, Ex [HT]
Capacity: unlimited
Min. number of students: unlimited
4EU+: no
Virtual mobility / capacity: no
State of the course: taught
Language: Czech, English
Note: enabled for web enrollment
Guarantor: prof. Mgr. Pavel Jungwirth, CSc., DSc.
Teacher(s): Lukasz Cwiklik
prof. Mgr. Pavel Jungwirth, CSc., DSc.
Annotation -
Introduction to molecular dynamics and Monte Carlo methods for simulating molecular systems. Suitable primarily for Ms. and PhD. students at PřF UK and MFF UK. For Erasmus teaching can be in English.
Last update: Jungwirth Pavel, prof. Mgr., CSc., DSc. (27.11.2017)
Literature - Czech

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.

Last update: Cwiklik Lukasz (18.02.2019)
Requirements to the exam - Czech

Zkoušku může skládat student/ka, který/á nejpozději 7 dnů předem předloží zpracovaný samostatný projekt z praktické části.
Zkouška je ústní v rozsahu probírané látky (viz sylabus).
Základem zkoušky je "obhajoba" samostatného projektu, důraz je kladen na porozumění použitým metodám a podstatě mezimolekulových interakcí v simulovaném systému.

V době koronavirové uzávěry probíhá studium formou individuálních konzultací na UOCHB spolu s domácími úkoly (četbou).

Last update: Jungwirth Pavel, prof. Mgr., CSc., DSc. (19.10.2020)
Syllabus -

1. 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, Leap-frog method etc.

4. Basics of Monte Carlo methods. Metropolis method of generation of the canonical ensemble.

5. Simulation protocol: 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.

7. Examples of use for solving practical problems in biophysics, surface science etc.



Within the class, there will be both theoretical lectures and practical demonstrations of computer simulations.

Last update: Cwiklik Lukasz (18.02.2019)
 
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