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Course, academic year 2022/2023
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Molecular dynamics II - NBCM347
Title: Molekulární dynamika II
Guaranteed by: Institute of Physics of Charles University (32-FUUK)
Faculty: Faculty of Mathematics and Physics
Actual: from 2020
Semester: winter
E-Credits: 5
Hours per week, examination: winter 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)
This course builds on “Molecular dynamics I” to dive into topics at the forefront of current research. It focuses on the treatment of nuclear quantum effects using path integral methods. Other topics include ab initio molecular dynamics and methodology for computationally efficient simulations. The material will be illustrated with readings from current literature followed by discussions. This course is suitable for Mgr. and Ph.D. students with basic knowledge of quantum mechanics and quantum statistical mechanics.
Course completion requirements -
Last update: RNDr. Ondřej Maršálek, Ph.D. (30.04.2020)

Class credit will be given for the successful execution of calculations in practical computational exercises and for earning at least 50 % points on homework. Homework should be handed in by email, the deadline for all homework for the semester is the date of the handing in of the exam project. Practical exercises are carried out independently by the students based on assignments, with the lecturer being available for consultation by email or video call.

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. The discussion can be carried out remotely by a video call.

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

● Tuckerman - Statistical Mechanics

● Thomas E. Markland and Michele Ceriotti, Nuclear quantum effects enter the mainstream, Nature Reviews Chemistry volume 2, Article number: 0109 (2018),

● Scott Habershon, David E. Manolopoulos, Thomas E. Markland, and Thomas F. Miller III, Ring-Polymer Molecular Dynamics: Quantum Effects in Chemical Dynamics from Classical Trajectories in an Extended Phase Space, Annual Review of Physical Chemistry, Vol. 64:387-413,

● Frenkel, Smit - Understanding Molecular Simulation

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

● Ab initio molecular dynamics

● Multiple time stepping propagation

● Imaginary-time path integrals

● Path integral molecular dynamics

● Equilibrium isotope effects

● Approximate time evolution from path integrals - centroid molecular dynamics and ring polymer molecular dynamics

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