SubjectsSubjects(version: 947)
Course, academic year 2023/2024
Molecular modelling - N320095
Title: Molekulové modelování
Guaranteed by: Department of Biochemistry and Microbiology (320)
Faculty: Faculty of Food and Biochemical Technology
Actual: from 2022
Semester: winter
Points: winter s.:3
E-Credits: winter s.:3
Examination process: winter s.:
Hours per week, examination: winter s.:2/0, Ex [HT]
Capacity: unknown / unknown (unknown)
Min. number of students: unlimited
Language: Czech
Teaching methods: full-time
Teaching methods: full-time
Is provided by: M320043
For type:  
Guarantor: Spiwok Vojtěch prof. Ing. Ph.D.
Raich Ivan doc. Dr. Ing.
Is interchangeable with: M320043
Examination dates   Schedule   
Annotation -
Last update: Spiwok Vojtěch prof. Ing. Ph.D. (19.06.2013)
The subject covers theoretical backgrounds and practical examples of application of computational methods on molecular systems, namely molecular mechanics and quantum mechanics. It includes small molecules, as well as biomolecules and supra-molecular systems.
Aim of the course -
Last update: Spiwok Vojtěch prof. Ing. Ph.D. (12.07.2013)

Students will be able to:

design, apply and analyse results of molecular modelling calculations (molecular mechanics, basic quantum chemistry methods, docking).

Literature -
Last update: Spiwok Vojtěch prof. Ing. Ph.D. (12.07.2013)

R: D.C. Young: Computational Chemistry: A Practical Guide for Applying Techniques to Real World Problems. John Wiley & Sons, Inc., 2002, ISBN: 9780471333685 (print), 9780471220657 (online)

Learning resources -
Last update: Spiwok Vojtěch prof. Ing. Ph.D. (04.07.2013)

Syllabus -
Last update: Spiwok Vojtěch prof. Ing. Ph.D. (12.03.2015)

1. 3D geometry, Cartesian coordinates, Z-matix, connectivity, PDB file

2. Inspection of 3D models, bond lengths, angles, torsions, rendering

3. Structure-potential energy relationship, different levels of theory, potential energy hypersurface

4. Molecular mechanics, ball-spring model, single point calculations

5. Schrödinger equation, wave function, approximative solutions, methods (including semi-empirical), variational methods, basis sets

6. Prediction of properties (charges, reaction kinetics and mechanisms, spectral and chiroptical properties)

7. Geometry optimization, local minima problem

8. Molecular vibrations, normal modes

9. Solvation, implicit and explicit solvent, continuum electrostatics

10. Molecular dynamics, PBC, NPT, NVT, thermostats, constraints

11. Sampling, data collection, analysis and visualisation

12. Mesoscopic simulations (coarse graining, Brownian simulations)

13. Free energy, metadynamics and related methods

14. Example studies

Registration requirements -
Last update: TAJ320 (25.09.2013)

Physical Chemistry

Teaching methods
Activity Credits Hours
Konzultace s vyučujícími 0.5 14
Účast na přednáškách 0.5 14
Příprava na přednášky, semináře, laboratoře, exkurzi nebo praxi 0.5 14
Práce na individuálním projektu 0.5 14
Příprava na zkoušku a její absolvování 1 28
3 / 3 84 / 84
Coursework assessment
Form Significance
Regular attendance 30
Defense of an individual project 10
Examination test 30
Oral examination 30