Material for the Molecular Dynamics (MD) simulations exercise in the Protein Science course.

Open the MD_Protein_Science.ipynb and read its contents before the exercise!

Downloading the git repository to desktop

git clone https://github.com/au-mbg/protein_science.git ~/Desktop/

cd ~/Desktop/protein_science

Activating conda environment to run Jupyter Notebook

module load miniconda3

conda activate /sw/common/miniconda3/envs/MD

You should see (MD) pop up at the beginning of your terminal line. This means that you are now in the conda environment called MD.

jupyter-lab MD_Protein_Science.ipynb

If you want to exit the notebook for any reason, in the terminal window press CTRL+C. You will be asked if you want it to shut down (answer y).

File structure

The two folders contain the same simulation runs, but with different atom selections:

1. Insulin_w_solvent: included protein + solvent

   • Insulin is centered in the middle of the simulation box

2. Insulin: only the protein

   • Insulin is centered in the middle of the simulation box, and its rotational and translational motions have been removed

There are two sets of simulations:

1. INS1

   • coordinate file: INS1.pdb

   • trajectory file: INS1.xtc

2. INS2

   • coordinate file: INS2.pdb

   • trajectory file: INS2.pdb