PřF:C7790 Intro. to Mol. Mod. - Course Information
C7790 Introduction to Molecular ModellingFaculty of Science
- 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).
Taught in person.
- RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor)
Mgr. Ivo Durník (seminar tutor)
- Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research - Faculty of Science
Supplier department: National Centre for Biomolecular Research - Faculty of Science
- Mon 16:00–17:50 C04/118
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 11/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30
- fields of study / plans the course is directly associated with
- there are 13 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Learning outcomes
- Student will be able to:
- create appropriate models of studied problems;
- perform basic quantum-chemical and molecular-mechanical calculations;
- calculate interaction energy;
- find the transition state of the elementary reaction and determine its activation energy;
- describe the dynamics of small molecular system;
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minima and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001. xxiii, 744. ISBN 0582382106. info
- CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004. xx, 596. ISBN 0470091819. info
- JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007. xx, 599. ISBN 9780470011874. info
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Follow-Up Courses
- Further comments (probably available only in Czech)
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
- Listed among pre-requisites of other courses
- Enrolment Statistics (recent)
- Permalink: https://is.muni.cz/course/sci/autumn2022/C7790