MBG wiki: Calculation of frame-to-frame rmsds

NOTE WELL : calculation of the rms deviation between each and every frame of two DCD files can be a lot of work. With, say, 10,000 frames in each DCD, you will have to least-squares superimpose 10,000 x 10,000 = 100 million pairs of structures. You can reduce the amount of calculation by (i) using CA-only DCD and PSF files, and (ii) by defining a step size of around 5 or 10.

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 gv carma.stdin.ps

giving :

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).