carma and catdcd can do the trick via a script named crossDCD. Here is an example (which assumes that you've already created a CA-only PSF file) :
carma -v -fit native.psf native.dcd
mv carma.fitted.dcd CA.dcd
crossDCD CA.psf CA.dcd CA.dcd 10
carma - < crossDCD.matrix
The file crossDCD.matrix is the actual rmsd matrix. This can be used to further analyse the trajectory(ies) (via for example a procedure known as cluster analysis, see Cluster analysis of trajectories).