C9926 Problems and issues of molecular modeling

Faculty of Science
Spring 2019
Extent and Intensity
2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: z (credit).
Teacher(s)
prof. RNDr. Robert Vácha, PhD. (lecturer)
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
Timetable
Mon 18. 2. to Fri 17. 5. Mon 15:00–16:50 C04/211
Prerequisites
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.
The capacity limit for the course is 10 student(s).
Current registration and enrolment status: enrolled: 1/10, only registered: 0/10, only registered with preference (fields directly associated with the programme): 0/10
Course objectives
Learn from the mistakes of others
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
  • The good, the bad and the user in soft matter simulations; DOI: 10.1016/j.bbamem.2016.02.004
  • Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions; DOI: 10.1016/S0006-3495(03)75094-2
Teaching methods
Study of the literature, presentation and discussion
Assessment methods
Presentation and discussion of the studied problem
Language of instruction
English
Further comments (probably available only in Czech)
Study Materials
The course is taught once in two years.
General note: S.
The course is also listed under the following terms Spring 2017, Spring 2021, Spring 2022, Spring 2025.
  • Enrolment Statistics (Spring 2019, recent)
  • Permalink: https://is.muni.cz/course/sci/spring2019/C9926