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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
