C9555 A Survival Guide to Simulations

Přírodovědecká fakulta
podzim 2023
Rozsah
1/2/0. 4 kr. Ukončení: z.
Vyučující
Denys Biriukov, Ph.D. (přednášející)
Ing. Ondřej Kroutil, Ph.D. (přednášející)
William Shakespeare Morton, PhD (přednášející)
Timothée Emmanuel Jonathan Rivel, Ph.D. (přednášející)
prof. RNDr. Robert Vácha, PhD. (přednášející)
Garance
prof. RNDr. Robert Vácha, PhD.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Rozvrh
Čt 10:00–10:50 C04/118, Čt 11:00–12:50 C04/118
Předpoklady
Basic knowledge of general chemistry, classical mechanics, and physical chemistry.
Omezení zápisu do předmětu
Předmět je otevřen studentům libovolného oboru.
Cíle předmětu
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.
Výstupy z učení
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.
Osnova
  • (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.
Výukové metody
Lectures & Practical Exercises
Metody hodnocení
Credits will be awarded based on a final simulation project.
Vyučovací jazyk
Angličtina
Další komentáře
Studijní materiály
Předmět je vyučován každoročně.
Předmět je zařazen také v obdobích podzim 2024.