9360-0239/01 – Molecular modeling using force fields (MMSP)

Gurantor departmentCNT - Nanotechnology CentreCredits10
Subject guarantordoc. Ing. Jonáš Tokarský, Ph.D.Subject version guarantordoc. Ing. Jonáš Tokarský, Ph.D.
Study levelpostgraduateRequirementChoice-compulsory type B
YearSemesterwinter + summer
Study languageCzech
Year of introduction2020/2021Year of cancellation
Intended for the facultiesFMTIntended for study typesDoctoral
Instruction secured by
LoginNameTuitorTeacher giving lectures
TOK006 doc. Ing. Jonáš Tokarský, Ph.D.
Extent of instruction for forms of study
Form of studyWay of compl.Extent
Full-time Examination 20+0
Part-time Examination 20+0

Subject aims expressed by acquired skills and competences

Student will be able to identify a problem solvable by molecular modeling, identify relevant data needed to build the initial model, apply a suitable molecular modeling strategy, discuss and interpret the results of molecular simulations

Teaching methods

Individual consultations


The aim of the course is to deepen the student's ability to recognize a problem solvable by molecular modeling methods. In the course of the subject will be discussed especially the questions of input experimental data, selection of appropriate modeling strategy, and interpretation results obtained by molecular modeling. Since the molecular modeling using force fields is used, the course is not focused on the electron properties of materials, but on their structure and behavior under given conditions. Practical exercises, which are the main content of the course, are focused on surface modification, intercalation, sorption, miscibility, but also on X-ray diffraction or infrared spectra simulation. The course will also provide students with examples of successful applications of molecular modeling methods in material research.

Compulsory literature:

SMIT, B. and D. FRENKEL. Understanding molecular simulation: from algorithms to applications. 2nd ed. San Diego: Academic Press, 2002. ISBN 978-0122673511 HINCHLIFFE, A. Molecular modelling for beginners. 2nd ed. Hoboken, NJ: Wiley, 2008. ISBN 978-0470513149 COMBA, P. a T. W. HAMBLEY. Molecular modeling of inorganic compounds. 2nd ed. Weinheim: Wiley-VCH, 2001. ISBN 3-527-297778-2

Recommended literature:

POSPÍŠIL, M. and M. VETEŠKA. Computational procedures in molecular dynamics. Materials Structure. 2012, vol. 19, no. 2, pp. 71-74

Way of continuous check of knowledge in the course of semester

The study results are verified continuously in the exercises. The results of exercises are processed in the form of five protocols (max. 4 credits per protocol, required minimum 2 credits per protocol). Individual semestral work is elaborated (max. 20 credits, required minimum 10 credits). Semester is completed by summation of credits from protocols and the semestral work (max. 40 credits, required minimum 20 credits). The oral exam follows (max. 60 credits, required minimum 31 credits).


Other requirements

Written protocols from practical exercises.


Subject has no prerequisities.


Subject has no co-requisities.

Subject syllabus:

Identification of problem solvable by molecular modeling using force fields. Identification, interpretation, and utilization of data from instrumental analytical methods for the needs of initial model preparation. Basic chemical calculations for initial model preparation. Choosing a modeling strategy for given problem. Interpretation of molecular modeling results and comparison with experimental data. Molecular modeling of intercalates (practical exercise). Molecular modeling of miscibility of selected substances (practical exercise). Molecular modeling of small molecule sorption (practical exercise). Molecular modeling of nanoparticles on inorganic substrate (practical exercise). Simulation of X-ray diffraction of inorganic and organic structures (practical exercises). Simulation of infrared spectra of selected substances (practical exercise).

Conditions for subject completion

Full-time form (validity from: 2020/2021 Winter semester)
Task nameType of taskMax. number of points
(act. for subtasks)
Min. number of points
Examination Examination  
Mandatory attendence parzicipation:

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Occurrence in study plans

Academic yearProgrammeField of studySpec.ZaměřeníFormStudy language Tut. centreYearWSType of duty
2022/2023 (P0719D270002) Nanotechnology K Czech Ostrava Choice-compulsory type B study plan
2022/2023 (P0719D270002) Nanotechnology P Czech Ostrava Choice-compulsory type B study plan
2021/2022 (P0719D270002) Nanotechnology P Czech Ostrava Choice-compulsory type B study plan
2021/2022 (P0719D270002) Nanotechnology K Czech Ostrava Choice-compulsory type B study plan
2020/2021 (P0719D270002) Nanotechnology K Czech Ostrava Choice-compulsory type B study plan
2020/2021 (P0719D270002) Nanotechnology P Czech Ostrava Choice-compulsory type B study plan

Occurrence in special blocks

Block nameAcademic yearForm of studyStudy language YearWSType of blockBlock owner