| Course Unit Code | 9600-1012/01 |
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| Number of ECTS Credits Allocated | 4 ECTS credits |
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| Type of Course Unit * | Choice-compulsory type A |
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| Level of Course Unit * | Second Cycle |
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| Year of Study * | Second Year |
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| Semester when the Course Unit is delivered | Summer Semester |
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| Mode of Delivery | Face-to-face |
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| Language of Instruction | Czech |
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| Prerequisites and Co-Requisites | Course succeeds to compulsory courses of previous semester |
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| Name of Lecturer(s) | Personal ID | Name |
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| KAL0063 | prof. RNDr. René Kalus, Ph.D. |
| VIT0060 | Mgr. Aleš Vítek, Ph.D. |
| Summary |
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| Students will learn the theoretical foundations of molecular modelling and will be introduced to the fields of Molecular Dynamics and Monte Carlo methods. |
| Learning Outcomes of the Course Unit |
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Upon the successful completion of the course, students will be able to:
- actively use basic concepts in the field of molecular simulations using Monte Carlo and Molecular Dynamics methods,
- implement simple models,
- perform computer simulations and analyse their results,
- independently extend the acquired knowledge in the field of study.
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| Course Contents |
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1. Summary of Classical Statistical Thermodynamics, Statistical Ensembles.
2. Summary of Classical Mechanics, Equations of Motion.
3. Intramolecular and Intermolecular Interactions, Force Fields.
4. Molecular Dynamics Methods for the NVE Ensemble.
5. Molecular Dynamics Methods for other Statistical Ensembles.
6. Numerical Solvers for Equations of Motion.
7. Markov Chains, Transition Matrices, Metropolis Algorithm.
8. Pseudorandom Number Generators.
9. Monte Carlo Methods for the NVT Ensemble.
10. Monte Carlo Methods for other statistical Ensembles.
11. Convergence Accelerating Approaches (parallel tempering).
12. Summary of Quantum Mechanics and Quantum Statistical Thermodynamics.
13. Quantum Monte Carlo methods. |
| Recommended or Required Reading |
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| Required Reading: |
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1.Nezbeda, I., Kolafa J., Kotrla M. Úvod do počítačových simulací. Metody Monte Carlo a molekulární dynamiky, Karolinum, Praha 2003, ISBN 80-246-0649-6.
2.Allen, M.P., Tildesley, D.J. Computer Simulations of Liquids. Oxford University Press, Oxford 1989, ISBN 0-19-855645-4.
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1.Nezbeda, I., Kolafa J., Kotrla M. Úvod do počítačových simulací. Metody Monte Carlo a molekulární dynamiky, Karolinum, Praha 2003, ISBN 80-246-0649-6.
2.Allen, M.P., Tildesley, D.J. Computer Simulations of Liquids. Oxford Science Publications, Oxford 1989, ISBN 0-19-855645-4.
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| Recommended Reading: |
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| 1.Hinchliffe, A., Molecular modelling for beginners, Second edition, John Wiley & Sons Ltd, Chichester 2008, ISBN 978-0-470-51313-2. |
| 1.Hinchliffe, A., Molecular modelling for beginners, Second edition, John Wiley & Sons Ltd, Chichester 2008, ISBN 978-0-470-51313-2. |
| Planned learning activities and teaching methods |
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| Lectures, Tutorials |
| Assesment methods and criteria |
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| Task Title | Task Type | Maximum Number of Points
(Act. for Subtasks) | Minimum Number of Points for Task Passing |
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| Credit and Examination | Credit and Examination | 100 (100) | 51 |
| Credit | Credit | | |
| Examination | Examination | 100 | 51 |