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2024-05-04
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2024-05-03
Editing revision 4 of Calculation of frame-to-frame rmsds
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<b>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.</b> /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) : <code> 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 </code> giving : [[image: frame-to-frame rmsd (graph)]] 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]]).
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