RMSD analysis

• To investigate the relative movements of the protein we are interested, we compute the RMSD of each frame to the first frame.

python frameRMSD.py

• The goal of simulated annealing is to get the model more accurate. we create a pdb file (named sa_protein.pdb) containing only protein atoms in the last frame of the trajectory file (processed.xtc) using Gromacs. To compute the RMSD of the sa_protein.pdb to the real structure (3eml.pdb).

python generateSaRMSD.py