[gmx-users] rmsd with average structure

[Prasad Gajula]

Dear Groamcs users,

I calcualted the average structure from the simulation trajectory. when I
calculate the rmsd of the protein to this average sturture, it is giving
average rmsd of 0.16 nm. But, it is not clear for me why the average
sturcture is never adapted rmsd near (or equal) to zero. I did not
calculate the rmsd with respect to the starting structure either.
Any clue?
Thanks in advance!