9600-1012/01 – Introduction to Molecular Simulations (UMS)

Gurantor departmentIT4InnovationsCredits4
Subject guarantorprof. RNDr. René Kalus, Ph.D.Subject version guarantorprof. RNDr. René Kalus, Ph.D.
Study levelundergraduate or graduateRequirementChoice-compulsory type A
Study languageCzech
Year of introduction2016/2017Year of cancellation
Intended for the facultiesFMTIntended for study typesFollow-up Master
Instruction secured by
LoginNameTuitorTeacher giving lectures
KAL0063 prof. RNDr. René Kalus, Ph.D.
VIT0060 Mgr. Aleš Vítek, Ph.D.
Extent of instruction for forms of study
Form of studyWay of compl.Extent
Full-time Credit and Examination 2+1
Part-time Credit and Examination 10+5

Subject aims expressed by acquired skills and competences

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.

Teaching methods



Students will learn the theoretical foundations of molecular modelling and will be introduced to the fields of Molecular Dynamics and Monte Carlo methods.

Compulsory literature:

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.

Recommended literature:

1.Hinchliffe, A., Molecular modelling for beginners, Second edition, John Wiley & Sons Ltd, Chichester 2008, ISBN 978-0-470-51313-2.

Way of continuous check of knowledge in the course of semester


Other requirements

No further requirements.


Subject has no prerequisities.


Subject has no co-requisities.

Subject syllabus:

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.

Conditions for subject completion

Full-time form (validity from: 2019/2020 Winter semester)
Task nameType of taskMax. number of points
(act. for subtasks)
Min. number of points
Credit and Examination Credit and Examination 100 (100) 51
        Credit Credit  
        Examination Examination 100  51
Mandatory attendence parzicipation: Project elaboration and its presentation, oral exam.

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Occurrence in study plans

Academic yearProgrammeField of studySpec.ZaměřeníFormStudy language Tut. centreYearWSType of duty
2021/2022 (N0719A270002) Nanotechnology MM1 P Czech Ostrava 2 Choice-compulsory type A study plan
2020/2021 (N0719A270002) Nanotechnology MM1 P Czech Ostrava 2 Choice-compulsory type A study plan
2019/2020 (N0719A270002) Nanotechnology MM1 P Czech Ostrava 2 Choice-compulsory type A study plan

Occurrence in special blocks

Block nameAcademic yearForm of studyStudy language YearWSType of blockBlock owner