Steps to follow for a MSM estimation:

    > python extractCoords.py 
        e.g. python extractCoords.py -w -resname AEN -t 50 --> extracts AEN's COM in trajectories of 50+1 steps (+1 for the initial) and writes traj_ligand files
        e.g. python extractCoords.py -atomIds 3223:C1:AEN 3224:C2:AEN 3225:C3:AEN --> extracts C1, C2 and C3 atoms

    > python prepareMSMFolders.py (optional in sequential runs)

    > python estimateDGAdaptive.py

    > gnuplot plotResults.gpl
