[gmx-users] Principal axes of inertia and g_principal

[nicola staffolani]

​Dear GMX community,

regarding the program g_principal and acknowledged the bug reported here
<http://permalink.gmane.org/gmane.science.biology.gromacs.user/66719>​
​, I would like to understand what the meaning of the output of this
program is.
So, left aside moi.dat, the output files are axis1.dat, axis2.dat &
axis3.dat.
Supposing that I have already corrected the output files (or reinstalled
GROMACS having fixed the bug in the source file as explained always here
<http://t110399.science-biology-gromacs-user.biotalk.us/g-principal-bug-or-very-bad-choice-of-filenames-t110399.html>),
in each of the files, for each time instant there are three coordinates: x,
y and z: what do they mean? My interpretation is that if I connect the
point, whose coordinates are those printed out in the output files, with
the origin of the Cartesian axes, then I get a line coinciding with the
corresponding (principal) axis: is this interpretation correct?

To get the principal axes, I have to diagonalize the moment of inertia
symmetric 3×3 matrix; one way to do it is by solving the 3rd order equation
for the eigenvalues: is this the way by which GROMACS finds then the
eigenvectors of the moment of inertia matrix, from which it calculates the
aforementioned coordinates?

Thank you in advance,

Nicola       ​

-- 
Nicola Staffolani PhD
Biophysics & Nanoscience Centre <http://www.unitus.it/biophysics>
Università della Tuscia
Largo dell'Università s.n.c., I-01100 Viterbo
email: n.staffolani at unitus.it
tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36