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

raja raja_28 at fastmail.us
Fri Jul 28 13:25:17 CEST 2006

```Hi Tsjerk,
Here is the script I am using. I already checked the value computed by
this script with manually computed value for small set of 3 eigen
vectors in each file. As you already know the formula, so please check
it up by yourself. More I am not a regular programmer so this script is
written for some quick solution, so please do not expect perfection in
usage of commands.
#---------------------------Perl script for computing R.M.S.I.P.
value----------------------------------------------------------
# each file "eig1.xvg" and "eig2.xvg" contain 10 eigenvectors
\$F1 = "eig1.xvg";
\$F2 = "eig2.xvg";
open(F1) or die("Could not open file.");
\$N1 = 0;
foreach \$line(<F1>)
{
\$A = \$line;
open(F2) or die("Could not open file");
foreach \$line(<F2>)
{
\$B = \$line;
\$N = (\$A*\$B)*(\$A*\$B);
print " \$N \n";
\$N1 = \$N1 + \$N ;
#print " \$N1 \n ";
}
close(F2)
}
print "The Value of N1 is \$N1 \n";
\$N1 = \$N1/10;
\$N1 = sqrt (\$N1);
print "\$N1";
close(F1) ;
#-------End of
code-------------------------------------------------------------------------------------------

With thanks !
B.Nataraj

On Fri, 28 Jul 2006 13:05:23 +0200, "Tsjerk Wassenaar"
<tsjerkw at gmail.com> said:
> Hi Raja,
>
> I really don't get it. From the definition it follows directly that if
> you have the same sets of eigenvectors, the RMSIP will be 1. Each
> eigenvector from a set gives an inproduct of 1 with itself and of 0
> with any of the others, yielding a total of 10 for the double sum...
> etc. If you use the same set twice, you probably have a bug in your
> script.
>
> Besides, from the definition it also follows that the RMSIP can not
> exceed 1. I think 3.5% error is quite a bit.
>
> Tsjerk
>
> On 7/28/06, raja <raja_28 at fastmail.us> wrote:
> > 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
> > > >
> > > > --
> > > > http://www.fastmail.fm - A fast, anti-spam email service.
> > > >
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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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> >   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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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