SubjectsSubjects(version: 955)
Course, academic year 2019/2020
Molecular modelling - M320043
Title: Molekulové modelování
Guaranteed by: Department of Biochemistry and Microbiology (320)
Faculty: Faculty of Food and Biochemical Technology
Actual: from 2019 to 2021
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: unlimited / unknown (unknown)
Min. number of students: unlimited
State of the course: taught
Language: Czech
Teaching methods: full-time
Teaching methods: full-time
Guarantor: Spiwok Vojtěch prof. Ing. Ph.D.
Raich Ivan doc. Dr. Ing.
Lankaš Filip doc. Ing. Ph.D.
Interchangeability : N320095
Examination dates   Schedule   
This subject contains the following additional online materials
Annotation -
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.
Last update: Kubová Petra (15.01.2018)
Aim of the course -

Students will be able to:

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

Last update: Kubová Petra (15.01.2018)
Literature -

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)

Last update: Kubová Petra (15.01.2018)
Learning resources -

Last update: Spiwok Vojtěch (18.12.2023)
Syllabus -

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

Last update: Kubová Petra (15.01.2018)
Registration requirements -

Physical Chemistry

Last update: Kubová Petra (15.01.2018)
Teaching methods
Activity Credits Hours
Konzultace s vyučujícími 0.5 14
Účast na přednáškách 1 28
Příprava na přednášky, semináře, laboratoře, exkurzi nebo praxi 0.5 14
Příprava na zkoušku a její absolvování 1 28
3 / 3 84 / 84
Coursework assessment
Form Significance
Regular attendance 10
Oral examination 90