structure @native.psf end dynamics analysis average asci=false input=fitted.dcd begin=0 skip=1 stop=2000000 reference=aver end write coordinates output=aver_and_rms.pdb end stop
The DCD file that you feed to xplor must have global rotations-translations removed.
Edit aver_and_rms.pdb and remove the header lines. Save the modified file. The B-factor column contains rms fluctuations for the corresponding atoms. View it :
rasmol aver_and_rms.pdb restrict not hydrogen cpk color temperature wireframe off cpk off cartoon
Use your editor to select the B-value column (ie the fluctuations) of the Cα atoms only and save them to file. Use xmgr to make a graph of how the rms fluctuations change across the structure.