[gmx-users] Representative structure from MD trajectories

[bipin singh]

Sir, thanks for your reply....
Yes I should have limited number of structure for a given point(pc1,pc2) but
in my case, I have taken pc1 and pc2 as a range of points where the
minima in FEL lies rather than a
single point.So I think it would be relevant to apply the clustering
as per your suggestion.Please let me
know whether I am correct or not..
But which clustering method would be better for clustering my MD
trajectories is also a question for me.
I read some papers in which they have mentioned that the average
linkage method works well for most
of the cases, is it same to the gromacs linkage method of clustering?

Please provide your suggestion.




On Sat, Sep 10, 2011 at 13:35, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Bipin,
>
> 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
> But you should only have a limited number of structures for a given point
> (pc1,pc2), so why not just visualize the ensemble?
>
> Hope it helps,
>
> Tsjerk
>
> On Sep 10, 2011 8:02 AM, "bipin singh" <bipinelmat at gmail.com> wrote:
>
> Hello,
>
> I have constructed a 2-d FEL using PC1 and PC2 as the reaction
> coordinates(by using g_sham).
> >From this 2-d FEL, I extracted the PC1 and PC2 (principal components)
> values corresponding to minimum free energy.
> Then I extracted the time during which system possess these PC's
> values( by looking at PC Vs time plot).
> Now I want to extract representative structures from these time
> length(for eg. 40ns to 70 ns) of MD trajectories.
>
>
> This question had been discussed previously but I am not able to find
> a consensus solution:
>
> There are three approaches discussed in the previous posts:
> (1)Use g_cluster with options -av(writes average) -cl and then
> minimize the structure
> (2)Use g_covar -av, and then minimize the average structure.
> (3)Use g_rmsf -ox, and minimize the structure
>
>
> Please suggest which approach should be used for this purpose.
>
>
>
>
> --
> -----------------------
> Thanks and Regards,
> Bipin Singh
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-- 
-----------------------
Thanks and Regards,
Bipin Singh