[gmx-users] only 4 zero eigvals for NMA (with 10^-6 emtol for l-bfgs)

[lloyd riggs]

I can imagine why you would go past the first few, but does it print the zero's or just negate them from the equation, as there 0?

Stephan
-------- Original-Nachricht --------
> Datum: Sun, 10 Mar 2013 14:34:52 -0500
> Von: Hyuntae Na <htna at hotmail.com>
> An: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Betreff: [gmx-users] only 4 zero eigvals for NMA (with 10^-6 emtol for	l-bfgs)

> Dear, This is the same issue that I asked last time. I wonder (1) if I
> setup the test wrong, (2) if NMA *can* have smaller than 6 eigenvalues even
> though the conformation of a protein is in equilibrium  in the enough degree,
> or (2) if it gromacs does not make it in equilibrium because of the limit
> of the tolerance that gromacs can take care of. Is there anyone who can
> give me an advice for this? I updated the sample location in the case that the
> previous Skype link is not available. I am studying several protein
> fluctuation proteins using NMA (Normal Mode Analysis). In the mean time, I found
> out in many cases that NMA hessian matrix has about 3-4 zero eigenvalues
> even though having 6 zero eigenvalues are expected. I tried to reduce the
> tolerance level lesser than 10^-6 for the l-bfgs minimization, but still it
> have only 4 zero eigenvalues. Following is the 9 smallest eigenvalues (you
> can see that it has only 4 close-to-zero eigenvalues):
> -1.8476593e-06-1.2164109e-06-1.4830436e-071.3104790e-061.1364704e+001.7418209e+002.2836573e+003.7218206e+004.4875873e+00
> Theoretically, NMA should have 6 zero eigenvalues which represents the
> freedom of the rotation and translation. I wonder why this happens.
>  
> Is there anyone who can help me for this problem?
>  
> In order to specify the case, I leave a link to download a zip file that
> contains files for one NMA tests having the problem: script, mdp, pdb, gro,
> topol, etc. The zip file also includes the eigenvalue/vector files.
> http://129.186.69.109/NMA-test.zip
>  
> Thank you very much.
>  
> -- Hyuntae
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