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

Fri Jul 28 13:35:48 CEST 2006

Hi Raja,

Okay, you're not using the eigenvectors, you're using the
eigenvalues... The eigenvectors are written to a .trr or .xpm file, as
NxN matrices.

You can try the attached script (which I got from Isabella Daidone) on
the .xpm file.

Good luck,

Tsjerk

On 7/28/06, raja <raja_28 at fastmail.us> wrote:
> 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
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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
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