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

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jul 28 11:32:04 CEST 2006

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,


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
+31 50 363 4336

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