Learning Outcomes:
- Understanding of the practical aspects of molecular simulations.
- Basics of the command-line interface and usage high-performance computing resources.
- Operating common computational chemistry packages to tackle real chemical problems.
- Preparation of systems for molecular dynamics simulations and troubleshooting the set up, simulations and analysis steps.
- Understanding of the limitations of the computational chemistry techniques used.
- Reporting of the methodology and observations in a condensed written format.
- Group working, encouraged and developed through the practicals.
Computational techniques have become an integral part of the research, with their importance and contribution to scientific discovery growing rapidly in recent years. The use of computational techniques in chemistry has made it possible to simulate chemical reactions and predict the properties of molecules with a high degree of accuracy. Additionally, molecular simulations have made it possible to study complex systems that are difficult, if not impossible, to study experimentally, such as large protein complexes, biological membranes, interactions of molecules and materials at the interface, processes in space or in extreme conditions. These methods have had a positive impact on society by accelerating the development of new drugs, materials, and technologies. Therefore, it is essential for students to have a solid understanding of computational techniques and their applications in modern scientific methods. This part of the course, focuses on molecular dynamics simulations, one of the most commonly used methodologies in current research.
Content:
Session 1: Introduction to Linux and command-line.
Session 2: Introduction to molecular dynamics simulations on a practical simulation of a protein.
Session 3: Molecular simulation set up of system with an interface.
Session 4: Beginning of the individual projects.
All the materials for the sessions are provided on GitHub.