Week 4¶
This week:¶
This week we start to perform our own molecular dynamics (MD) simulations using Gromacs. The simulation data will be analyzed and visualized, and we will work through some basic procedures.
The first system to be simulated is simply water. Although this sounds simple, this is a very important step since it introduces some general procedures and, importantly, in our late simulations during the course we need to solvate more complex systems.
Important
When we set up simulations, practical matters such as being able to estimate how long the simulation takes, how much storage space it needs, and so on are important questions to answer prior to starting the actual simulation. It is (unfortunately) not uncommon to run out of storage pace or to overestimate how large a system one can simulate.
For data analysis, we will use Python, Gromacs’ tools and VMD.