Hi Nicola, On Thu, 11 Sep 2014, nicola staffolani wrote:
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?
Yes, that is correct. In other words, they are the coordinates of the point P=O+v, where O is the origin and v is the vector of unit norm that points along that principal axis. Of course, for graphical representation purposes, you would displace each of those 3 principal axis vectors to make them point away from the center of mass of your system, since the whole idea is to get a reference frame which is "natural" to that system (e.g., see Goldstein or any other book on rigid body mechanics).
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?
As I pointed in the links you mentioned, I didn't look very deep into the GROMACS code, but the vectors that g_principal writes (after the correction) are exactly the ones obtained from the diagonalization you describe. But check it yourself for a simple case. My rule of thumb: never trust an analysis tool until you check it yourself... :)
Best, Antonio
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.staffol...@unitus.it tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
-- Antonio M. Baptista Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa Av. da Republica - EAN, 2780-157 Oeiras, Portugal phone: +351-214469619 email: bapti...@itqb.unl.pt fax: +351-214411277 WWW: http://www.itqb.unl.pt/~baptista --------------------------------------------------------------------------
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