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

[David van der Spoel]

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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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se