Thanks Tsjerk<br><br><div class="gmail_quote">On Thu, Dec 15, 2011 at 4:55 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Hi Vijayan.R,<br>
<br>
Not really. NMA also assumes linear relationships.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div class="HOEnZb"><div class="h5"><br>
On Thu, Dec 15, 2011 at 10:48 PM, R.S.K.Vijayan <<a href="mailto:biovijayan@gmail.com">biovijayan@gmail.com</a>> wrote:<br>
> Hi Tsjerk<br>
><br>
> Many thanks for your response. Do you think NMA is worth considering in such<br>
> cases like this?????<br>
><br>
> Regards<br>
> Vijayan.R<br>
><br>
> On Thu, Dec 15, 2011 at 3:39 PM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:<br>
>><br>
>> Hi Vijayan R.,<br>
>><br>
>> > What i infer from this is that the cumulative variance experienced by<br>
>> > the<br>
>> > top 10 PC is hardly ~ 30 %.<br>
>><br>
>> Not experienced...; It's the variance captured by the first ten PC's.<br>
>><br>
>> > a) does this imply inadequate sampling by MD or a limited conformational<br>
>> > change happening in the system????<br>
>><br>
>> No, not at all. It shows that the motions in your system can not be<br>
>> adequately captured by linear combinations of atom fluctuations. The<br>
>> system may be too flexible and/or there may be a lot of rotational<br>
>> motion.<br>
>><br>
>> > b) is it wise to consider the Nucleic acid during essential dynamics or<br>
>> > should it be discared and only the Protein BB or CA be considered.<br>
>><br>
>> Analysis with and without nucleic acids are just two different things.<br>
>><br>
>> Cheers,<br>
>><br>
>> Tsjerk<br>
>><br>
>> --<br>
>> Tsjerk A. Wassenaar, Ph.D.<br>
>><br>
>> post-doctoral researcher<br>
>> Molecular Dynamics Group<br>
>> * Groningen Institute for Biomolecular Research and Biotechnology<br>
>> * Zernike Institute for Advanced Materials<br>
>> University of Groningen<br>
>> The Netherlands<br>
>> --<br>
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<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
--<br>
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</div></div></blockquote></div><br>