[gmx-users] rmsd with average structure

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 10 19:49:41 CET 2008

Prasad Gajula wrote:
> 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?
the average structure is unphysical, it may have long bonds etc.

> Thanks in advance!
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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

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