[gmx-users] Re: gmx-users Digest, Vol 45, Issue 30

Prasad Gajula prasad.gajula at uni-osnabrueck.de
Thu Jan 10 20:06:02 CET 2008

Dear Dr. David,
Thank you very for the reply.
When i looked the energy minimized average structure it looks just fine.

>> 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?
> the average structure is unphysical, it may have long bonds etc.

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