> Is there any way to get RMSD over each residues using ptraj after a MD
>simulation?
I suppose you could do it for each residue, one at a time. You can specify the part of the molecule in the mask. For example, you could do something like this:
trajin production.1.mdcrd
trajin production.2.mdcrd
reference average.inpcrd
rms reference mass out rmsdFromAverageResidue1.txt :1 nofit
rms reference mass out rmsdFromAverageResidue2.txt :2 nofit
rms reference mass out rmsdFromAverageResidues3-8.txt :3-8 nofit
Hope this helps!
-Ty
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