Beginning at 9:00 AM on 10th July 2023.
Lectures will take place on working days (Monday to Friday) from 10th to 21st July. Each day, classes start at 9:00 and end at about 16:00 (latest). Small refreshments will be provided during coffee breaks. Lunches and accommodation are not provided by the organizers.

Theoretical lessons combined with practical exercises will cover the following topics:

• Basics from phenomenological and statistical thermodynamics.
• Physical foundations of interaction within and between atoms.
• How to build suitable models ranging from small to very large systems.
• Chemistry models, including quantum mechanics (QM), molecular mechanics (MM), coarse-grained mechanics (CG), and their hybrid versions, in particular QM/MM.
• Sampling techniques for the free energy calculation, employing an ideal gas model and potential of mean force (PMF) methods, including umbrella sampling, metadynamics, adaptive biasing force, and their accelerated versions by a multiple-walker approach.
• Impact of collective variables on calculated free energies.
• How to simulate biomolecular systems properly.
• Impact of pH on ionizable groups and reconstruction of experimentally unresolved protein structure parts.
• Protein structure prediction by machine learning methods (AlphaFold, ESMFold).
• Docking to prepare protein/substrate complexes.
• Simulations employing ReaxFF reactive force field.

Software used during the course: Gaussian, Orca, Amsterdam Modeling Suite (formerly known as ADF), AMBER, Gromacs, PLUMED, PMFLib, MODELLER, AutoDock, AutoDock Vina, Dock, PROPKA, AlphaFold, OmegaFold, ESMFold, and many others.

The summer school will take place at National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Czech Republic. The classes will be in a computer classroom with workstations using the Linux operating system.

Since Linux is a mainstream OS on computational clusters and supercomputers employed for molecular modelling, we will provide students with all the necessary information on how to work in this environment. We will cover essential work in graphical and command-line Linux environments employing local and remote sessions. Thus, no prior knowledge of working in Linux is necessary (but it will be a plus). Students can bring their computers (laptops or tables). We will show how to access Linux computers remotely by various techniques (ssh, putty, WinSCP, [no]VNC) from MS Windows, macOS, Linux, and Android OSes. In addition, students will get access to the national MetaCentrum supercomputing center. The access will be granted for two months, allowing students to use obtained knowledge during summer on their projects.