[gmx-users] R.M.S.I.P for identical eigenvectors not equal to 1 ?

[raja]

Hi Tsjerk,
Thanks for your reply. I used identical values of 10 eignevectors in two
different file to compute r.m.s.i.p. I have pasted the link of the
article from where I used the formula for r.m.s.i.p. More for some other
cases of non-identical values, it slightly exceeds the value of 1 (e.g.,
1.0352), Which I am thinking due to some numerical problem. But I am
confident that my script exactly following what the formula indicated in
the article as pasted hereunder.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1304087

With thanks !
B.Nataraj

On Fri, 28 Jul 2006 11:32:04 +0200, "Tsjerk Wassenaar"
<tsjerkw at gmail.com> said:
> Hi Raja,
> 
> Did you use the same eigenvectors from the same simulation over the
> same stretch of time? For two (parts of a) simulation(s) of the same
> system, the RMSIP value will only converge to one in the limit of
> infinite time, or on long time scales at least. The eigenvectors
> obtained from two different (parts of) simulations can vary if
> different parts of the conformational space are sampled or simply if
> the sampling is different, which will be almost always for a limited
> stretch of time.
> 
> Best regards,
> 
> Tsjerk
> 
> On 7/28/06, raja <raja_28 at fastmail.us> wrote:
> > Dear all,
> >
> > I have written small perl script to compute R.M.S.I.P.(Root mean square
> > internal product) for comparing two eigen vectors set from two different
> > simulation. I compared first 10 eigen vectors of each set. The strange
> > thing is that while I compare eigen vectors of same simulation, it is
> > showing a value of 0.54, but literature says, r.m.s.i.p of 1 indicates
> > that the sets are identical, while a value of 0 indicates that the
> > eigenvectors are orthogonal. I also confirmed my script validity by
> > manually computing the R.M.I.P for small set of values.
> >
> > Could any body explain me a bit regarding this issue?
> >
> > With thanks!
> > B.Nataraj
> > --
> >   raja
> >   raja_28 at fastmail.us
> >
> > --
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> 
> -- 
> 
> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747AG Groningen, The Netherlands
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-- 
  raja
  raja_28 at fastmail.us

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