Hi,
Thank you for your response. What I want to do is to add values of the
first eigenvector elements into a reference structure and visualize it
in cones. Therefore, the opposite signs can cause opposite directions,
although the relative signs are ok. Can I still to show them in this
kind of cones?
Thanks,
Qi
-----Original Message-----
From: owner-amber.scripps.edu on behalf of Adrian Roitberg
Sent: Mon 6/9/2008 8:51 AM
To: amber.scripps.edu
Subject: Re: AMBER: Problem of Ptraj analyze matrix
Dear Qi,
The signs are completely irrelevant, except when in comparison between
eigenvector elements and between eigenvectors.
These are akin 'phases' in quantum mechanical wavefunctions, where the
absolute sign of an orbital does not matter per-se, but must be
consistent to make sure the orbitals are orthogonal.
So, in your case:
> 1 6682.90154
> -0.02344 0.00701 0.00270 -0.00799 0.00716 0.00631
> 0.00676
and
> 1 6682.90154
> 0.02344 -0.00701 -0.00270 0.00799 -0.00716 -0.00631
> -0.00676
are the same because the only important thing regarding signs is that
the relative signs are ok.
Cheers
Adrian
Qi Yan wrote:
> Hi,all:
>
> When calculating the first eigenvector, I found a problem. I used two
> different ptraj.in files and got an opposite result of eigenvector.
>
> first ptraj1.in (I just calculated the first eigenvector):
>
> rms first .CA
> matrix covar name cvmat .CA out cvmat.dat
> analyze matrix cvmat out eigen_covar.dat vecs 1
>
> first result:
>
> 1 6682.90154
> -0.02344 0.00701 0.00270 -0.00799 0.00716 0.00631
> 0.00676
> 0.01184 0.01257 0.00844 0.01400 0.01116 0.00726
> 0.01468
> ... ...
>
> second ptraj2.in (the difference is that I calculate the first two
> eigenvectors, but the very first eigenvector is what I want):
>
> rms first .CA
> matrix covar name cvmat .CA out cvmat.dat
> analyze matrix cvmat out eigen_covar.dat vecs 2
>
> second result:
>
> 1 6682.90154
> 0.02344 -0.00701 -0.00270 0.00799 -0.00716 -0.00631
> -0.00676
> -0.01184 -0.01257 -0.00844 -0.01400 -0.01116 -0.00726
> -0.01468
> ... ...
>
> We can see the sign of values is opposite. I have no idea why this
> happened? Does anybody point me out?
>
> Thanks in advance,
>
> Qi
>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project
Department of Chemistry
Senior Editor. Journal of Physical Chemistry
American Chemical Society
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
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Received on Wed Jun 11 2008 - 06:07:27 PDT
