LECTURE
1. What is molecular modelling.
2. An overview of the use of molecular modeling on specific major publications, with emphasis on state-of-the-art approaches.
3. Computer simulations vs. experiment. Model building, data interpretation, validation of results.
4. Visualization and presentation tools.
5. Classical models: Molecular mechanics. Concept of force field, contributions to force field, binding and non-binding interactions, parameterization.
6. Classical Dynamics: Equations of motion and their integration, concept of barostats, thermostats, periodic boundary conditions, steps to successful molecular dynamics simulation setup, simulation protocols.
7. Introduction to modeling from first principles.
8. Hartre-Fock method, post-HF methods.
9. Introduction to semiempirical methods.
10. Calculation of thermodynamic quantities.
11. Interaction of electromagnetic radiation with matter.
12. Good scientific practice in molecular modelling.
13. Exam.
PRACTICAL PART
1. Preparation of the working environment.
2. Working with literature and electronic resources.
3. Formats of coordinate system notation, molecule topology. Construction and visualization of molecular structures of chemical and biological systems using commonly used programs.
4. Visualization and presentation tools.
5. Comparison of force fields, parameter tuning.
6. Short molecular dynamics simulations of chemical/biological systems.
7. Calculation of the potential energy surface of small systems. Optimization vs. single point calculations.
8. Intermolecular complexes - stability, interaction energy, self-assembly.
9. Adsorption of molecules on the surface of low-dimensional structures.
10. Calculation of frequencies and thermodynamic quantities.
12. Modeling spectra of molecular systems (UV-Vis, etc.).
12. Work on a credit project.
13. Evaluation of the credit project.
1. What is molecular modelling.
2. An overview of the use of molecular modeling on specific major publications, with emphasis on state-of-the-art approaches.
3. Computer simulations vs. experiment. Model building, data interpretation, validation of results.
4. Visualization and presentation tools.
5. Classical models: Molecular mechanics. Concept of force field, contributions to force field, binding and non-binding interactions, parameterization.
6. Classical Dynamics: Equations of motion and their integration, concept of barostats, thermostats, periodic boundary conditions, steps to successful molecular dynamics simulation setup, simulation protocols.
7. Introduction to modeling from first principles.
8. Hartre-Fock method, post-HF methods.
9. Introduction to semiempirical methods.
10. Calculation of thermodynamic quantities.
11. Interaction of electromagnetic radiation with matter.
12. Good scientific practice in molecular modelling.
13. Exam.
PRACTICAL PART
1. Preparation of the working environment.
2. Working with literature and electronic resources.
3. Formats of coordinate system notation, molecule topology. Construction and visualization of molecular structures of chemical and biological systems using commonly used programs.
4. Visualization and presentation tools.
5. Comparison of force fields, parameter tuning.
6. Short molecular dynamics simulations of chemical/biological systems.
7. Calculation of the potential energy surface of small systems. Optimization vs. single point calculations.
8. Intermolecular complexes - stability, interaction energy, self-assembly.
9. Adsorption of molecules on the surface of low-dimensional structures.
10. Calculation of frequencies and thermodynamic quantities.
12. Modeling spectra of molecular systems (UV-Vis, etc.).
12. Work on a credit project.
13. Evaluation of the credit project.