1. Use paste to merge the two data files from carma (carma.Rgyration.dat AND carma.distances) so that each column is pasted next to the other
2. Use an editor to remove the columns that contain the frame number, or if you would rather use unix, tell it something like awk '{print $2 ” ” $4}' file_from_paste > new_file
3. Then, you need to make a grid out of the two columns in order to make a nice plot. The program grid will do the trick.

paste carma.Rgyration.dat carma.distances > Rg_vs_N-C.dat
joe Rg_vs_N-C.dat peptide.dat
grid peptide.dat peptide.grid
carma -col - < peptide.grid
mv carma.stdin.ps peptide.ps

Montage can help you prepare a nice image of all the postscript files you created so that you can compare them (and hopefully come to some conclusions, which is why you went through all that trouble in the first place!!!)

montage -title 'Rg vs N-C distance' -bordercolor cyan -background black -tile 3x4 -fill cyan -label RWMDF_1 RWMDF_1.ps -label RWQDY RWQDY.ps -label RDWDR RDWDR.ps -label RWMDF_2 RWMDF_2.ps -label RWTDQ_1 RWTDQ_1.ps -label RDGDR RDGDR.ps -label RWMDF_3 RWMDF_3.ps -label RWTDQ_2 RWTDQ_2.ps -label RYTDQ RYTDQ.ps -label RWMDF_hel RWMDF_hel.ps -label RWTDQ_hel RWTDQ_hel.ps -label AAAAA AAAAA.ps all.ps