[gmx-users] only 4 zero eigvals for NMA

[Hyuntae Na]

Dear, 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.https://skydrive.live.com/redir?resid=37B4631A59B510F!34933 Thank you very much. -- Hyuntae