Week 3¶
This week:¶
This week we will take us to molecular dynamics (MD) simulations. The aim is to learn the what MD is, to install Gromacs, the software that we will use for our simulations and to install VMD (Visual Molecular Dynamics). We start the explorations of molecular systems with VMD as visualization is one of the key components. Importantly, VMD is not only for visualization, it also provides a framework for data analysis and it can be used for both simulational and experimental data.
One the main aims this week is to understand the basic protocol and concepts of MD simulations. The actual simulations will be started next week.
Important
This week, you will learn how to compile software starting from the source code. For that, we will install C/C++ compilers and compile Gromacs for our simulations. You will also learn the basics of
cmake, a software to create software builds.The concepts that we learn this week are fundamental and will be elaborated and put into practise during the next two weeks.