[gmx-users] write the eigenvectors of a PCA analysis

edesantis edesantis at roma2.infn.it
Fri Mar 23 11:10:22 CET 2018

Dear gromacs users,

I am performing PCA on my system,
since I am a beginner of this kind of analysis and I want to check if I 
understood well the theory behind,
I'd like to know if is there the possibility to print into an ascii file 
the eigenvectors generated by gmx covar and stored in the .trr file.

I found in the gmx anaeig the flag -comp ( according to the manual: 
"plot the vector components per atom of eigenvectors -first to -last"), 
I am not sure if the result of this flag are really the 
eigenvectors...in particular what puzzles me is the fact that if I try 
to perform the dot plot among the vectors I have, they are not 
orthogonal (and to me, since the covariance matrix should be symmetric 
and with real elements, by definition the autovectors should be an 
orthonormal basis set)

can you help me please?
thank you in advance,

Emiliano De Santis

Emiliano De Santis, PhD student

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