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Course, academic year 2022/2023
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Molecular dynamics I - NBCM346
Title: Molekulární dynamika I
Guaranteed by: Institute of Physics of Charles University (32-FUUK)
Faculty: Faculty of Mathematics and Physics
Actual: from 2020
Semester: summer
E-Credits: 5
Hours per week, examination: summer s.:2/1, C+Ex [HT]
Capacity: unlimited
Min. number of students: unlimited
Virtual mobility / capacity: no
State of the course: taught
Language: Czech, English
Teaching methods: full-time
Teaching methods: full-time
Guarantor: RNDr. Ivan Barvík, Ph.D.
RNDr. Ondřej Maršálek, Ph.D.
Annotation -
Last update: prof. RNDr. Marek Procházka, Ph.D. (28.01.2019)
Molecular dynamics has become a powerful tool of modern physics and chemistry that is essential for our understanding of complex molecular systems and the condensed phase in general. This course introduces the fundamental methodology of molecular dynamics, with emphasis on its foundation in classical mechanics and statistical mechanics. Exercises offer an opportunity to immediately apply lecture material in practical computation. The course is suitable for Mgr. and Ph.D. students with knowledge of classical mechanics and basic statistical mechanics.
Course completion requirements -
Last update: RNDr. Ondřej Maršálek, Ph.D. (30.10.2019)

Class credit will be given for the successful execution of calculations in practical computational exercises.

The exam will be given for independent completion of a computational project. The student will perform calculations and prepare a report. After handing in the report, they will answer questions on the project within the scope of the topics covered by the course. The topic of the project will be chosen from a list provided by the lecturer, or based on the interest of the student within the topics covered by the class, after consulting with the lecturer.

Literature -
Last update: prof. RNDr. Marek Procházka, Ph.D. (30.04.2019)

Tuckerman - Statistical Mechanics: Theory and Molecular Simulation, Oxford University Press, 2010 ISBN 9780198525264

Frenkel, B. Smit: Understanding Molecular Simulations: From Algorithms to Applications - Academic Press: San Diego, 2001, ISBN 0122673514

Syllabus -
Last update: prof. RNDr. Marek Procházka, Ph.D. (28.01.2019)

● Numerical propagators for MD derived from the Liouville operator

● Thermostats and barostats, simulating the NVT and NpT ensembles

● Molecular interactions and their numerical evaluation

● Calculating static properties from MD, link to thermodynamics, error estimation

● Energy transfer in MD simulations, local and global thermostats

● Calculating dynamical properties from time correlation functions

● Constraints and restraints

● External biases and non-equilibrium simulations

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