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Molecular Dynamics and Monte Carlo Methods - NBCM051

Title:	Metody molekulové dynamiky a Monte Carlo
Form of teaching:	lecture+practicals
Guaranteed by:	Department of Chemical Physics and Optics (32-KCHFO)
Faculty:	Faculty of Mathematics and Physics
Actual:	from 2026
Duration in semesters:	1
Semester:	winter
E-Credits:	5
Hours per week, examination:	winter s.:2/1, C+Ex [HT]
Capacity:	unlimited
Maximum number of enrolled students:	unlimited
Min. number of students:	unlimited
4EU+:	no
Virtual mobility / capacity:	no
State of the course:	taught
Language:	Czech
Teaching methods:	full-time
Repeated enrollment:	2 / 2 / 2 / 2

Guarantor:	prof. dr hab. Lukasz Stanislaw Cwiklik, Ph.D.
Teacher(s):	prof. dr hab. Lukasz Stanislaw Cwiklik, Ph.D.
Class:	Fyzika
Classification:	Physics > Biophysics and Chemical Physics

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Annotation -

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.

Last update: JUNGWIRT (29.05.2007)

Course completion requirements -

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

Last update: Procházka Marek, prof. RNDr., Ph.D. (14.05.2020)

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: Procházka Marek, prof. RNDr., Ph.D. (28.01.2019)

Course assessment methods and requirements for successful completion, grading scheme -

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

Last update: Procházka Marek, prof. RNDr., Ph.D. (14.05.2020)

Syllabus -

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.

Last update: JUNGWIRT (30.05.2007)