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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)
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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)
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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)
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Předmět je zakončen ústní zkouškou Last update: Cibulková Jana (03.12.2023)
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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)
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https://web.vscht.cz/spiwokv/molmod/ https://web.vscht.cz/~spiwokv/modelovani2/ Last update: Spiwok Vojtěch (18.12.2023)
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Physical Chemistry Last update: Cibulková Jana (03.12.2023)
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