[gmx-users] Normal modes are not orthogonal???

[Kumaran Baskaran]

Hi,
    I am trying to understand normal mode analysis in gromacs. I just
took one amino acid(Glycine), energy minimized then calculated normal
mode eigenvectors as described in Gromacs manual(grompp,mdrun,g_nmeig).
Then I calculated the inner product between them using 'g_anaeig'.
example: g_anaeig -v eigenvec.trr -v2 eigenvec.trr -inpr
I would expect all diagonal elements are 1 and the off-diagonal elements
are zero. But I didn't get that. Could anyone explain to me what went
wrong?

PS: I did everything in double precision

Thanks in advance..


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