C9555 A Survival Guide to Simulations

Faculty of Science
Autumn 2024
Extent and Intensity
1/2/0. 4 credit(s). Type of Completion: z (credit).
Teacher(s)
Denys Biriukov, Ph.D. (lecturer)
Ing. Ondřej Kroutil, Ph.D. (lecturer)
William Shakespeare Morton, PhD (lecturer)
Timothée Emmanuel Jonathan Rivel, Ph.D. (lecturer)
prof. RNDr. Robert Vácha, PhD. (lecturer)
Guaranteed by
prof. RNDr. Robert Vácha, PhD.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
Basic knowledge of general chemistry, classical mechanics, and physical chemistry.
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives
The course is designed to provide practical lessons that emphasize hands-on learning, with little to no coding knowledge required. Students will gain proficiency in using the GROMACS molecular dynamics engine, along with scientific programming in Python as well as utilizing other software tools and libraries, including VMD, CHARMM-GUI, MDAnalysis, and more.
Learning outcomes
A student after the successful completion of the course will be able to:
(1) Understand both the fundamentals and advanced concepts of molecular dynamics simulations;
(2) Construct simulation models for intricate biological systems;
(3) Execute molecular dynamics simulations using cutting-edge software on contemporary hardware;
(4) Analyze simulations with established tools and skills acquired in Python programming;
(5) Present simulation results suitable for a peer-reviewed scientific publication.
Syllabus
  • (1) Brief introduction to Linux, Bash, and other necessary tools for performing and analyzing computer simulations;
  • (2) Introduction to VMD --- graphical visualization of modeled systems --- and Python --- top-one scientific programming language;
  • (3) Advanced usage of molecular dynamics engine Gromacs tailored for biological applications:
  • (3a) Utilization of Gromacs built-in pre- and post-processing tools for system construction and simulation analysis;
  • (3b) Building of simulation models for biological membranes and molecules, including protein structures predicted by AlphaFold, using a range of online and offline tools, such as CHARMM-GUI or Avogadro, and the derivation of required force field parameters (e.g., atomic partial charges via CGenFF or SwissParam);
  • (3c) Execution of molecular dynamics for typical biological systems, incorporating lipid membranes, proteins, peptides, ligands, and ions at both all-atom and coarse-grained levels;
  • (3d) Applications of common free energy methods, including umbrella sampling, metadynamics, and accelerated weight histogram, using Gromacs capabilities or Gromacs along with PLUMED library;
  • (4) Crafting and employing analysis scripts, which includes programming in Python and visualization using xmgrace and Matplotlib.
Teaching methods
Lectures & Practical Exercises
Assessment methods
Credits will be awarded based on a final simulation project.
Language of instruction
English
Further Comments
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Autumn 2023.
  • Enrolment Statistics (Autumn 2024, recent)
  • Permalink: https://is.muni.cz/course/sci/autumn2024/C9555