AMBER Archive (2008)

Subject: AMBER: Problem of Ptraj analyze matrix

From: Qi Yan (kid1412_at_uab.edu)
Date: Mon Jun 09 2008 - 08:37:01 CDT

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

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