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 <h...@hotmail.com> > An: "gmx-users@gromacs.org" <gmx-users@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 > > -- > 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 -- 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
