This course provides a comprehensive introduction to Molecular Dynamics (MD) simulations and Molecular Structure modeling, focusing on both theoretical principles and hands-on computational approaches. Students will explore classical mechanics, interatomic forces, numerical integration methods, thermodynamic ensembles, and advanced simulation techniques applied to materials science, biophysics, and chemistry.
Laboratory sessions will focus on practical applications of the previous week's lecture topics. Each student will lead one lab session, implementing simulations using GROMACS, LAMMPS, Python-based tools (MDAnalysis, Ovito, VMD), and exploring data analysis methods.
By the end of the course, students will be able to:
✅ Understand and implement fundamental MD algorithms
✅ Apply force fields and interaction models in molecular simulations
✅ Utilize MD software to simulate real-world physical systems
✅ Analyze and interpret MD trajectories and thermodynamic properties
✅ Develop custom scripts for data analysis and visualization
