AMBER Archive (2008)

Subject: Re: AMBER: Problem of Ptraj analyze matrix

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Mon Jun 09 2008 - 08:51:42 CDT

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_at_qtp.ufl.edu
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