It is a common practice to check if your MD computations have converged by matching the Experimental Structure factor with the structure factors provided in the PDB file. Each PDB file gives a value of dynamic structural factor in the 11th column of the PDB file, which can be matched to outputs of your

More on structure factor at – Structure Factor Wiki
Example – Fig 5 of the paper – Anisotropy of fluctuation dynamics of proteins with an elastic network model.

One can compute the same for there MD trajectories using g_rmsf in Gromacs suite of MD programmes.

Download File – PDBStructFactorReader.pl
Step 1 : Rename pdb file of interest to ‘mypdb.pdb’
or, change the line in the perl code to your filename – $inputFile = ‘mypdb.pdb’;
Step 2 : Type – perl atomfluctuate.pl
Step 3 : xmgrace -nxy *.xvg (This will allow you to visulaise the *.xvg in xmgrace)