FB810 Problems and Issues of Molecular Modeling

Faculty of Science
Spring 2021
Extent and Intensity
2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: z (credit).
Taught online.
doc. RNDr. Robert Vácha, PhD. (lecturer)
Guaranteed by
doc. RNDr. Robert Vácha, PhD.
Department of Condensed Matter Physics - Physics Section - Faculty of Science
Contact Person: doc. RNDr. Robert Vácha, PhD.
Supplier department: Department of Condensed Matter Physics - Physics Section - Faculty of Science
C7790 Computat. Chem. and Molec. I
Frequent use of software for molecular modelling
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives
The course is focused on issues (limitations, errors, and artifacts), which has been observed and documented in molecular simulations. The main objective of the course is to provide the students with the ability to:
- learn from the mistakes of others
- understand limitations and errors of parameterizations and simulation conditions
- apply the obtained knowledge to analysis of molecular simulations
Learning outcomes
Student will be able to:
- understand the origin of the issues of molecular simulations
- analyze simulations for existence of the issues
- identify conditions where the issues can be expected
- learn from the previous mistakes
  • 1. Thermostats
  • - flying ice cube
  • - Equipartition theorem
  • - hot solvent cold solute
  • - stochastic thermostats and dynamics
  • 2. Long range interactions
  • - cut off
  • - charge neutrality of the system
  • - dipole in the system
  • 3. Forcefiled
  • - parametrisation
  • - mixing rules
  • - polarization catastrophe
  • - implicit solvent
  • 4. External field
  • - perpetum mobile
Teaching methods
Study of the provided literature, presentation and discussion of the issues at the classes
Assessment methods
For successful completion is required: attendance at least 80%, active participation in all discussions, presentation of at least two issues and being able to answer the given questions
Language of instruction
Further Comments
Study Materials
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Autumn 2019, Autumn 2020, autumn 2021, Spring 2022, Spring 2023.
  • Enrolment Statistics (Spring 2021, recent)
  • Permalink: https://is.muni.cz/course/sci/spring2021/FB810