Re: [AMBER] representing structure from equilibrium

From: Daniel Roe <>
Date: Mon, 11 May 2015 14:09:46 -0600

On Mon, May 4, 2015 at 10:35 AM, newamber list <> wrote:
> Another way someone suggested me is Clustering analysis. As far as I
> googled this term, one gets few clusters and one can choose lowest RMSD
> structure from centroid of most populated cluster. I am just wondering
> would this be a good way of choosing best representing structure?

Representative structures (which have lowest cumulative distance to
all frames in a cluster) are already output by the
'repout'/'singlerepout' keywords. Centroids are not written, but you
can think of average structures as the centroid where coordinate
metrics are concerned.

> Also cpptraj manual suggests there are two algorithms to choose. Which one
> I should use in my case. Also, when someone says 'distance from centroid'
> does it usually means RMSD? I am confused with terminologies used.

There are actually 3 clustering algorithms in cpptraj now: kmeans,
hieragglo, and dbscan. In the context of clustering, the distance
metric is RMSD by default - if you choose something else (like 'data')
then the distance refers to that.


> Thanks for any help.
> Jiom
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon May 11 2015 - 13:30:03 PDT
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