516-8818/01 – Introduction to molecular simulations (UMS)

Gurantor departmentInstitute of PhysicsCredits5
Subject guarantordoc. RNDr. Dalibor Ciprian, Ph.D.Subject version guarantordoc. RNDr. Dalibor Ciprian, Ph.D.
Study levelundergraduate or graduateRequirementChoice-compulsory
Study languageCzech
Year of introduction2013/2014Year of cancellation2015/2016
Intended for the facultiesHGFIntended for study typesFollow-up Master
Instruction secured by
LoginNameTuitorTeacher giving lectures
CIP10 doc. RNDr. Dalibor Ciprian, Ph.D.
TRO70 Mgr. Jana Trojková, Ph.D.
Extent of instruction for forms of study
Form of studyWay of compl.Extent
Full-time Graded credit 2+2

Subject aims expressed by acquired skills and competences

The course objective is to introduce the basic principles and methods of molecular simulations.

Teaching methods

Individual consultations


The course is oriented on pratical applications, after the presentation of fundamental principles the individual project-oriented work is intended.

Compulsory literature:

Frenkel D., Smit, B.: Understanding Molecular Simulation – 2nd. Ed., Academic Press , NewYork, 2002, ISBN 978-0122673702

Recommended literature:

Rapaport, D.C.: The Art of Molecular Dynamics Simulation, Cambridge UP, Cambridge 1995, ISBN 978-0-521-82568-9 Ciccotti, G., Frenkel, D., McDonald I.R. (edit.): Simulation of Liquids and Solids: Molecular Dynamics and Monte Carlo Methods in Statistical Mechanics, North-Holland, Amsterdam 1987, ISBN 0-444-87062-8.

Way of continuous check of knowledge in the course of semester

Discussion with students during the lessons


No e-learinig available

Other requirements

Systematic individual off-classroom study is assumed.


Subject has no prerequisities.


Subject has no co-requisities.

Subject syllabus:

1. The most important applications of statistical methods in physics, particle ensembles 2. Atoms, molecules, force interactions, description of molecules, degrees of freedom, intermolecular interactions 3. Lattice, continuum, classical and quantum models 4. Molecular dynamics principles 5. Basic principles of Monte Carlo method 6. Classification of quantities, average values and their simulations 7. Pseudo-experiments, the choice of methods, boundary conditions, ensemble size 8. Basic methods for classical systems 9. Qunatum simulations 10. Software and hardware resources, freeware packages 11. Practical aspects of simulations, time analysis, error estimation 12. Practical computations oriented on simple problems using molecular dynamics amd Monte Carlo (MATLAB, QWALK, etc) 13. Introducyion to MATERIAL STUDIO software package

Conditions for subject completion

Full-time form (validity from: 2013/2014 Winter semester, validity until: 2015/2016 Summer semester)
Task nameType of taskMax. number of points
(act. for subtasks)
Min. number of points
Graded exercises evaluation Graded credit 100  51
Mandatory attendence parzicipation:

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Occurrence in study plans

Academic yearProgrammeField of studySpec.ZaměřeníFormStudy language Tut. centreYearWSType of duty
2015/2016 (N1701) Physics (1702T001) Applied physics P Czech Ostrava 2 Choice-compulsory study plan
2014/2015 (N1701) Physics (1702T001) Applied physics P Czech Ostrava 2 Choice-compulsory study plan
2013/2014 (N1701) Physics (1702T001) Applied physics P Czech Ostrava 2 Choice-compulsory study plan

Occurrence in special blocks

Block nameAcademic yearForm of studyStudy language YearWSType of blockBlock owner