Re: [AMBER] clustering

From: Sowmya Indrakumar <>
Date: Wed, 1 Feb 2017 11:41:39 +0000

Dear Daniel and Bill,
Thank you for your suggestions.
I was expecting RMSD to increase with the cluster number, for instance RMSD of the representative structure to the average structure should be the least considered to the last cluster representative structure to the average). Since here, the frames are partitioned into distinct clusters, we don't take into account any reference structure.

But as you suggested, comparing to the average structure doesn't make sense if there is a lot of changes.
It is still not clear how frames are put into distinct cluster, does it compare all the frames and then assign them to various clusters?

From: Bill Ross []
Sent: Tuesday, January 31, 2017 7:11 PM
To: AMBER Mailing List
Subject: Re: [AMBER] clustering

Not sure if it has been pointed out, but average structures from
trajectories can be quite unrealistic if the system has interesting
changes going on.


On 1/31/17 9:59 AM, Daniel Roe wrote:
> On Tue, Jan 31, 2017 at 10:03 AM, Sowmya Indrakumar <> wrote:
>> running the above commands gives me 5 representative structures. It is not very clear to me what is it taking as the reference structure. Comparing the five generated representative pdb structure to the average pdb (from the trajectory) does not give show any trend in RMSD.
> The representative structure of each cluster is the frame with the
> lowest cumulative "distance" (in your case RMSD) to every other frame
> in the cluster. A cluster representative is just that; it's supposed
> to be representative of what that cluster looks like (although this
> may not always be the case). I can see how comparing representative
> structures to the average structure of the cluster could be
> informative ('avgout', 'avgfmt'), but it's not clear to me what
> insight you can gain from comparing representatives to the overall
> average structure.
> -Dan

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