C7790 Introduction to Molecular Modelling

Faculty of Science
Autumn 2022
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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021.
  • Enrolment Statistics (recent)
  • Permalink: https://is.muni.cz/course/sci/autumn2022/C7790