Am Sonntag, 4. Februar 2007 14:01 schrieb
Gohlke.bioinformatik.uni-frankfurt.de:
> Hi,
>
> we have been looking into the iRED part recently. We have also changed
> it such that now all eigenvectors/values are available (among other
> things). I will prepare a patch on Monday and distribute it.
Attached please find a patch for ptraj of Amber 9 concerning the iRED part.
Now all eigenvectors will be obtained, a bug related to the ordering of iRED
eigenvectors is removed, and the Cm(t->T) information is calculated (see eq.
A20 in JACS 2002, 124, 4522).
Best regards
Holger
>
> Best regards
>
> Holger
>
> Quoting "David A. Case" <case.scripps.edu>:
> > On Fri, Feb 02, 2007, Francois Theillet wrote:
> >> I have a problem with the treatment of the iRED method in ptraj (AMBER
> >> 8):
> >>
> >> I have a system of n vectors (i.e. a nxn covariance matrix), and I
> >> obtain only n-1 eigenvectors (and eigenvalues) instead of the hoped n.
> >> The sum of the eigenvalues is not exactly equal to n, but around
> >> n-lambda(n-1) (with lamda(n-1) the associated eigenvalue of the n-1th
> >> eigenvector).
> >> (I tried several n, the result is identical. If I precise that I want k
> >> eigenvectors (k<n), I obtain the first k eigenvectors correctly. With
> >> k>n, I obtain n-1 eigenvectors)
> >
> > This question (I think) has come up before:
> >
> > http://amber.ch.ic.ac.uk/archive/200501/0154.html
> >
> > The ptraj code uses an arpack routine to compute eigenvalues/vectors,
> > which seems to be limited to n-1 results. For PCA analysis, this is not
> > really a limitation; I'm not sure whether the same is true for iRED or
> > not. Please let
> > us know if you really need that last eigenvector: we can put it on a list
> > of things to look at in the next round of ptraj updates.
> >
> > ...thanks for the report....dac
> >
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--
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Juniorprofessor fuer Molekulare Bioinformatik
J.W. Goethe-Universitaet
Fachbereich Biowissenschaften
Institut für Zellbiologie und Neurowissenschaft
Max-von-Laue-Str. 9
60438 Frankfurt/Main
Germany
Tel.: (+49) 69-798-29411; Fax: (+49) 69-798-29527
Email: gohlke.bioinformatik.uni-frankfurt.de
URL: http://www.uni-frankfurt.de/~hgohlke
++++++++++++++++++++++++++++++++++++++++++++++++++
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Received on Wed Feb 07 2007 - 06:07:21 PST
