Lab 4: Simulation of water 2: Physical properties of water¶
Learning goals:
To get confident in setting up simple MD simulations
To gain experience in the basic protocols applied in MD simulations
To learn how to analyze physical properties using MD data
To learn how to use Gromacs’ indexing
To be able to make simple comparisons between experiments and simulations
Keywords: Molecular dynamics, physical properties, experiments vs simulations, radial distribution function, mean square displacement
Note:
You will need to consult the Gromacs manual
You will need to search literature for experimental data
You will need to estimate how large systems and how long you can simulate on your computer
The quantities we analyze are familiar from your other courses. This is how they emerge from real data. We will discuss them during the lectures this week.
As before, have your data and directories clearly organized and ensure that Gromacs is available for you.
The rest of the lab is simple: Pick up the assignment (number 5) from OWL and work throurgh it. The purpose of this lab is the get you going with independent work now that you have learned the basics. These skills will be used in the follow-up assignments as well as in the final projects (some of the analyses will be very closely related). No step-by-step instrcutions are provided.