This one-day course will take place in groups of 2-3 students. Dates will be individually fixed (March 2022) after the corresponding Lecture has ended.
Molecular dynamics simulations are a method to describe the dynamics of macro-molecules such as proteins, lipids or synthetic polymers. The movement of every atom is calculated on a computer by numerically integrating Newton's equations of motion.
This course aims to introduce the fundamental methods to you. Therefore, you are going to simulate a short polymer chain, a "toy-model" that behaves similarly to a small protein. The steps necessary to set up a simulation system will be performed. Subsequently, you will be introduced to the analysis methods, e. g. the calculation of structural order parameters, interaction energies, and free energy profiles.