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

[Tsjerk Wassenaar]

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
>> --
>> 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
>
>
>
> --
> 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.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands