[gmx-users] rmsd with average structure

Prasad Gajula prasad.gajula at uni-osnabrueck.de
Thu Jan 10 19:44:23 CET 2008

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!

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