On 2011-02-03 16.41, Kumaran Baskaran wrote:
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
How far off is it?
Thanks in advance..
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