SubjectsSubjects(version: 954)
Course, academic year 2023/2024
Molecular Modelling - AM320043
Title: Molecular Modelling
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
State of the course: taught
Language: English
Teaching methods: full-time
Teaching methods: full-time
Guarantor: Spiwok Vojtěch prof. Ing. Ph.D.
Raich Ivan doc. Dr. Ing.
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: Cibulková Jana (03.12.2023)
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: Cibulková Jana (03.12.2023)
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: Cibulková Jana (03.12.2023)
Learning resources -

Last update: Spiwok Vojtěch (18.12.2023)
Requirements to the exam - Czech

Předmět je zakončen ústní zkouškou

Last update: Cibulková Jana (03.12.2023)
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: Cibulková Jana (03.12.2023)
Registration requirements -

Physical Chemistry

Last update: Cibulková Jana (03.12.2023)