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Course, academic year 2018/2019
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Molecular dynamics: the fundamentals - NBCM346
Title in English: Molekulární dynamika: základy
Guaranteed by: Institute of Physics of Charles University (32-FUUK)
Faculty: Faculty of Mathematics and Physics
Actual: from 2018 to 2018
Semester: winter
E-Credits: 3
Hours per week, examination: winter s.:2/1 C+Ex [hours/week]
Capacity: unlimited
Min. number of students: unlimited
State of the course: taught
Language: Czech, English
Teaching methods: full-time
Guarantor: 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 their foundation in classical mechanics and statistical mechanics. All the material will be illustrated with examples from current research. Exercises offer an opportunity to immediately apply the content of the lectures in practical simulations.
Literature -
Last update: prof. RNDr. Marek Procházka, Ph.D. (30.04.2019)

● Tuckerman - Statistical Mechanics

● Allen, Tildesley - Computer Simulation of Liquids

● Frenkel, Smit - Understanding Molecular Simulation

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

● Statistical mechanics as the foundation of MD

● Liouville operator, numerical propagators for MD

● Molecular interactions - force fields, ab initio methods

● Thermodynamic ensembles, thermostats and barostats

● Equilibrium static properties from molecular dynamics, link to thermodynamics

● Energy transfer, local and global thermostats

● Linear response theory and dynamical properties

● Constraints and restraints

● External biases and non-equilibrium simulations

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