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

[R.S.K.Vijayan]

Thanks Tsjerk

On Thu, Dec 15, 2011 at 4:55 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Vijayan.R,
>
> Not really. NMA also assumes linear relationships.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Dec 15, 2011 at 10:48 PM, R.S.K.Vijayan <biovijayan at gmail.com>
> wrote:
> > 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
> >> --
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> >
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>
> --
> 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
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