[gmx-users] Eigenvalue values from PCA (a general question)

[R.S.K.Vijayan]

Hi Tsjerk

Many thanks for your response. Do you think NMA is worth considering in
such cases like this?????

Regards
Vijayan.R

On Thu, Dec 15, 2011 at 3:39 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Vijayan R.,
>
> > What i infer from this is that the cumulative variance experienced by
> the
> > top 10 PC is  hardly ~ 30 %.
>
> Not experienced...; It's the variance captured by the first ten PC's.
>
> > a) does this imply inadequate sampling by MD or a limited conformational
> > change happening  in the system????
>
> No, not at all. It shows that the motions in your system can not be
> adequately captured by linear combinations of atom fluctuations. The
> system may be too flexible and/or there may be a lot of rotational
> motion.
>
> > b) is it wise to consider the Nucleic acid during essential dynamics or
> > should it be discared and only the Protein BB or CA be considered.
>
> Analysis with and without nucleic acids are just two different things.
>
> Cheers,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111215/0a32de39/attachment.html>