[gmx-users] Fwd: Question => g_anaeig -first -last

[Tsjerk Wassenaar]

Hi Lin,

As these questions are not directly related to the tutorial, the
gromacs user list is the better place for them.

There are indeed as many eigenvectors in the .trr file as there are
-values in the .xvg file, and they are matching series.

The files you get for the extreme projections correspond to the set of
eigenvectors specified through -first to -last. In your case that
means the first ten eigenvectors.

The covariance matrix is positive semidefinite, which means that it
may have eigenvalues equal to zero. In your case, you'll get six zero
eigenvalues for the six degrees of freedom you remove by fitting the
trajectory. Due to limited numerical precision, these may turn out
slightly negative.

Cheers,

Tsjerk


---------- Forwarded message ----------
From: Chih-Ying Lin <chihying2008 at gmail.com>
Date: Mon, May 16, 2011 at 4:33 AM
Subject: Question => g_anaeig -first -last
To: Tsjerk Wassenaar <tsjerkw at gmail.com>




Hi Tsjerk:
I am doing your Tutorial and have a question about g_covar and a_anaeig.
I issued the following two commands.
g_covar_mpi -s 1LW9-MD.tpr -f 1LW9-MD.xtc -o eigenvalues.xvg -v
eigenvectors.trr -ascii covariances.dat
g_anaeig_mpi -v eigenvectors.trr -s 1LW9-MD.tpr -f 1LW9-MD.xtc -first
1 -last 10 -extr extreme-first-last.gro

There are 1476 eigenvalues in the eigenvalues.xvg and they are listed
from the max to min.
I supposed there are 1476 eigenvectors in eigenvectors.trr , right ????
Are those eigenvectors are listed corresponding to the the list of the
eigenvalues from the max to min ????
For the command, g_anaeig -first 1  -last 10  ...... , I will get 10
sets of .gro files.
Will those structures in the .gro files correspond to the top 10
eigenvalues ????

By the way, there are 6 negative eigenvalues in the eigenvalues.xvg.
I don't know why because you told me all eigenvalues are positive ????
Thank you very much
Lin










-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands