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

[Hyuntae Na]

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