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

[David van der Spoel]

Prasad Gajula wrote:
> Dear Dr. David,
> Thank you very for the reply.
> When i looked the energy minimized average structure it looks just fine.
> ??
but you did not say energy minimized... check the rmsd between average 
and minimized average structure as well.

Maybe you want to do a clustering analysis instead?
> 
> 
>>> 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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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se