[gmx-users] Principal axes of inertia and g_principal

nicola staffolani n.staffolani at unitus.it
Thu Sep 11 11:53:39 CEST 2014

​Dear GMX community,

regarding the program g_principal and acknowledged the bug reported here
​, 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 &
Supposing that I have already corrected the output files (or reinstalled
GROMACS having fixed the bug in the source file as explained always here
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

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