Hi Tsjerk<br><br>Many thanks for your response. Do you think NMA is worth considering in such cases like this?????<br><br>Regards<br>Vijayan.R<br><br><div class="gmail_quote">On Thu, Dec 15, 2011 at 3:39 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>
<div class="im"><br>
> What i infer from this is that the cumulative variance experienced by the<br>
> top 10 PC is hardly ~ 30 %.<br>
<br>
</div>Not experienced...; It's the variance captured by the first ten PC's.<br>
<div class="im"><br>
> a) does this imply inadequate sampling by MD or a limited conformational<br>
> change happening in the system????<br>
<br>
</div>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>
<div class="im"><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>
</div>Analysis with and without nucleic acids are just two different things.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<span class="HOEnZb"><font color="#888888"><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>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></span></blockquote></div><br>