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

Fri Feb 4 07:53:34 CET 2011

```These are the actual values extracted from xpm image
Diagonal element 0.34,0.6,0.8..(which is supposed to be 1.0)
Off-diagonal elements 0.3,0.21,0.01,...(which is supposed to be zero)

1. Maximum force at the end of energy minimization is of the order of
2.1x10^-10 (Is it sufficient? I can't go below that it says "reached
machine precision")

2. Energy minimization is done using l-bfgs (cg didn't give the lowest
energy I tried all three)

3. I used the .trr file from energy minimization to calculate normal
modes(for double precision)

4. Just a cross check: I ran normal md in glycine, then calculated
eigenvectors using covariance matrix(mdrun,g_covar then g_anaeig) and
then inner product between them. This was perfect. I get a neat diagonal
and all off diagonals are zero.

On Thu, 2011-02-03 at 19:20 +0100, David van der Spoel wrote:
> 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
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