Today we'll be learning to analyze our MD simulation trajectories with the Python tool MDAnalysis. You'll be working with a wildtype and mutated version of the profilin protein from Recitation 2 and analyzing how the mutation affects the RMSD and RMSF of the residues throughout the simulation. Follow the Colab notebook linked below and fill in the necessary code blocks to do the following:
Make a copy of the notebook so your changes are saved!!
Basic (✓):
- Align the trajectory files
- Calculate RMSD between the first frame of the trajectorys and the other frames
- Upload the plot to GradeScope with your name
Extra (✓+):
- Calculate the RMSF of the protein atoms across both simulations
- Map the RMSF values of each residue onto the Py3DMol visualization (color residues by RMSF). If you prefer, you may use pyMOL.
- Your visualization should highlight the site of the mutation and have an appropriately scaled color map.
- Upload your RMSF plot and structure image to GradeScope. Include a caption interpreting the figure.