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There are many different ways to analyse MD simulations and different tools to do so. For visual inspection of the trajectories I would use VMD or pymol. I like to script most of my analysis and therefore would recommend using either MDtraj or MDAnalysis. For a more sophisticated analysis of your trajectories, I would recommend having a look at Markov state model (MSM) analysis and in particular have a look at the ipython notebook tutorials provided with pyEMMA. An alternative package is MSMBuilder.
A very simple analysis would be looking at the root mean square deviations (RMSD) of the backbone from a simulation trajectory. The following snippets of python allow you to compute RMSD with MDtraj, it is however recommended to take a good look at the tutorials provided with all the different analysis packages.
import mdtraj as md
import matplotlib.pylab as plt
t = md.load('traj000000001.dcd', top='1AKI.parm7')
top = md.load_topology('../FESetup_tut/protein/1AKI/protein.pdb')
select = top.select("protein and backbone")
rmsds = md.rmsd(t, t, 0, atom_indices=select)
plt.plot(t.time*0.001, rmsds)
plt.xlabel('t in [ns]')
plt.ylabel('RMSD in [nm]')
plt.show()The plot should then look something like this:
Happy analysing your MD trajectories!
