Hi Ankita, Please provide the commands you've run and the screen output from g_covar.
Cheers, Tsjerk On Thu, Jun 6, 2013 at 3:44 PM, Ankita naithani <ankitanaith...@gmail.com>wrote: > Hi, > > I wanted to know about the eigenvectors and eigenvalues. I recently > performed the principal component analysis (only the backbone into > consideration) on a trajectory of 2000 residues. I obtained 15641 > eigenvectors and 17928 eigenvalues. There is a difference in the number, > which I am not quite sure off (perhaps that has to do with eigenvalue for > each eigenvector, and the eigenvector has 3 co-ordinates x,y,z. I know I > may be wrong completely but since there are 15641 eigenvectors, then > shouldn't there by only 15641 eigenvalues for those eigenvectors) > > My second problem lies that I am trying to extract information or say RMSF > values for the first 10 eigenvectors (10 slowest modes) and the last 10 > eigenvectors (fastest modes) and there I face segmentation fault. I can get > information on the first 10 but when I try last 10 with the command as > follows: > > g_anaeig -v eigenvec.trr -eig eigenval.xvg -rmsf eig_rmsf.xvg -first 15631 > > [where -first should have the starting eigenvector ] > > (I choose, 15631 since I want the plot for last 10 but I get segmentation > fault, which is also to do with the fact that the eigenval.xvg has 17928 > values. This number doesn't match and so, maybe the plot is from > 15631-17928). This has further confused me about the slowest and fastest > modes (and somehow I do need information on the first 10 slowest modes and > 10 fastest modes). In a broad way, the slowest modes would be the ones with > high eigenvalues say, first 10 eigenvectors in eigenval.xvg would give the > slowest 10 modes and the last 10 in eigenval.xvg should give the fastest 10 > modes. > > Here, again I feel quite confused because eigenval.xvg has 17928 entries > and in the legend, it says that x axis is the eigenvector index and y axis > is eigenvalue index so it leaves me quite perplexed about the problem. > > I am sorry for this extremely long and confusing post, but any help in this > regard would be really beneficial. > > > Kind regards, > > Ankita > > -- > Ankita Naithani > -- > 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 > -- Tsjerk A. Wassenaar, Ph.D. -- 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
