As long as you know which frames have a particular RMSD value greater than your threshold, then you can use a simple cpptraj input to extract those frames to a new trajectory file by just copying and pasting the frame numbers. If the RMSD is too unstable my simple input may not be the most efficient way.

That being said, you can try using the following Amber cpptraj input:

parm x.prmtop

trajin x.mdcrd *frames*

trajout y.mdcrd

run