[gmx-users] Eigenvector and eigenvalues

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jun 6 15:49:06 CEST 2013

Hi Ankita,

Please provide the commands you've run and the screen output from g_covar.



On Thu, Jun 6, 2013 at 3:44 PM, Ankita naithani <ankitanaithani at 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 at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Tsjerk A. Wassenaar, Ph.D.

More information about the gromacs.org_gmx-users mailing list