<p>Hi Bipin,</p>
<p>The averages from (2) and (3) are the same and may be far from realistic. Minimizing an average structure may not always yield a structure that is relevant or representative of the ensemble. I would suggest clustering<br>
But you should only have a limited number of structures for a given point (pc1,pc2), so why not just visualize the ensemble?</p>
<p>Hope it helps,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Sep 10, 2011 8:02 AM, "bipin singh" <<a href="mailto:bipinelmat@gmail.com">bipinelmat@gmail.com</a>> wrote:<br><br>Hello,<br>
<br>
I have constructed a 2-d FEL using PC1 and PC2 as the reaction<br>
coordinates(by using g_sham).<br>
>From this 2-d FEL, I extracted the PC1 and PC2 (principal components)<br>
values corresponding to minimum free energy.<br>
Then I extracted the time during which system possess these PC's<br>
values( by looking at PC Vs time plot).<br>
Now I want to extract representative structures from these time<br>
length(for eg. 40ns to 70 ns) of MD trajectories.<br>
<br>
<br>
This question had been discussed previously but I am not able to find<br>
a consensus solution:<br>
<br>
There are three approaches discussed in the previous posts:<br>
(1)Use g_cluster with options -av(writes average) -cl and then<br>
minimize the structure<br>
(2)Use g_covar -av, and then minimize the average structure.<br>
(3)Use g_rmsf -ox, and minimize the structure<br>
<br>
<br>
Please suggest which approach should be used for this purpose.<br>
<br>
<br>
<br>
<br>
--<br>
-----------------------<br>
Thanks and Regards,<br>
Bipin Singh<br>
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