C6760 Molecular Dynamics

Faculty of Science
Spring 2006
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
Teacher(s)
Mgr. Jaromír Toušek, Dr. (lecturer)
Guaranteed by
Mgr. Jaromír Toušek, Dr.
Department of Chemistry – Chemistry Section – Faculty of Science
Prerequisites
Physical chemistry I and II.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 22 fields of study the course is directly associated with, display
Course objectives
The aim of the course molecular dynamics is to explain main principles and approaches used in the molecular dynamics simulations. This course deals with the following topics: Newtonian dynamics. Hamiltonian dynamics. Phase-space trajectories. Determination of macroscopic properties. Monitoring equilibration. Periodic boundary conditions. Hard spheres. Soft spheres - Lennard-Jones model. Finite difference methods.
Syllabus
  • 1. Introduction - molecular dynamics, computer simulation methods, comparsion of molecular dynamics and other somputer simulation methods. 2. Newtonian dynamics, Hamiltonian dynamics - Newton equations of motion, Hamiltonian equations of motion. 3. Phase space trajectories - classification of dynamical systems, stability of dynamical systems. 4. How the phase-space trajectories are used - determination of macroscopic properties, equilibrium state, obtaining property values from simulation. 5. Fundamental distributions - distribution of velocities, Maxwell-Boltzmann distribution, distribution of instantaneous property values. 6. Periodic boundary conditions - primary cell, image cell, translation vector, coordinate transformations. 7. Hard spheres - kinematics of hard sphere collisions, elastic collisions, calculation of postcollision velocities and collision times. 8. Hard spheres - simulation algorithm, system of units, initial positions and velocities, evaluation of macroscopic properties, reliability of results. 9. Monitoring equilibration - positional disorder, velocity distribution, Boltzmann's H-function. 10. Finite-difference methods - Euler's method, Taylor expansion, truncation and round-off errors, algorithmic stability. 11. Algorithms for molecular dynamics - Runge-Kutta methods, Verlet's algorithm, predictor corrector algorithms. 12. Soft spheres - Lennard Jones model, shifted-force potential, neighboor lists. 13. Static properties - simple thermodynamic properties, thermodynamic response functions, radial distribution function. 14. Dynamic properties - time correlation functions, transport coefficients.
Literature
  • ALLEN, M. P. and D. J. TILDESLEY. Computer simulation of liquids. Oxford: Clarendon Press, 1997, xix, 385. ISBN 0198556454. info
  • LEACH, Andrew R. Molecular modelling : principles and applications. 1st pub. Essex: Longman, 1996, xvi, 595. ISBN 0582239338. info
Assessment methods (in Czech)
Výuka probíhá týdně. Ukončení - písemná a ústní zkouška.
Language of instruction
Czech
Further comments (probably available only in Czech)
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2000, Spring 2002, Spring 2004, Spring 2005, Spring 2007, Spring 2008.
  • Enrolment Statistics (Spring 2006, recent)
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