C9926 Problems and issues of molecular modeling

Faculty of Science
Spring 2025
Extent and Intensity
2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: z (credit).
In-person direct teaching
Teacher(s)
prof. RNDr. Robert Vácha, PhD. (lecturer)
doc. Mgr. Jan Havliš, Dr. (assistant)
Guaranteed by
prof. RNDr. Robert Vácha, PhD.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Robert Vácha, PhD.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
C7790 Intro. to Mol. Mod.
Frequent use of software for molecular modelling
Course Enrolment Limitations
The course is offered to students of any study field.
The capacity limit for the course is 10 student(s).
Current registration and enrolment status: enrolled: 0/10, only registered: 0/10, only registered with preference (fields directly associated with the programme): 0/10
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
Syllabus
  • 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

Literature
  • Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions; DOI: 10.1016/S0006-3495(03)75094-2
  • The good, the bad and the user in soft matter simulations; DOI: 10.1016/j.bbamem.2016.02.004
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
English
Further comments (probably available only in Czech)
The course is taught once in two years.
The course is taught: every week.
General note: S.
The course is also listed under the following terms Spring 2017, Spring 2019, Spring 2021, Spring 2022.
  • Enrolment Statistics (recent)
  • Permalink: https://is.muni.cz/course/sci/spring2025/C9926