I printed all small 50 eigenvalues, and their first 9 are listed as follows as before:* -1.8476593e-06* -1.2164109e-06* -1.4830436e-07* 1.3104790e-06* 1.1364704e+00* 1.7418209e+00* 2.2836573e+00* 3.7218206e+00* 4.4875873e+00 As you see, the first three of them are negative and close to zero, which can be considered as zero. do you know any reason of this, having only 4 (close to) zero eigenvalues ?? -- Hyuntae > Message: 3 > Date: Sun, 10 Mar 2013 23:10:05 +0100 > From: "lloyd riggs" <lloyd.ri...@gmx.ch> > Subject: Re: [gmx-users] only 4 zero eigvals for NMA (with 10^-6 emtol > for l-bfgs) > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <20130310221005.162...@gmx.net> > Content-Type: text/plain; charset="utf-8" > > > 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
