Re: [AMBER] Trouble understanding DBSCAN clustering algorithm

From: Daniel Roe <>
Date: Fri, 8 May 2015 08:24:49 -0600


On Fri, May 8, 2015 at 8:06 AM, Juan Eiros Zamora
<> wrote:
> I have read the Amber manual but I don't grasp the difference between
> the default distance metric (rms) and dme. Out of curiosity, what
> exactly is the difference between best-fit coordinate RMSD and
> distance-RMSD?

RMSD is the deviation between a target and reference set of
coordinates. DME is the deviation between internal distance pairs in a
target and reference set of coordinates. In my experience the
difference between best-fit RMSD and DME is pretty small, and the
latter is usually much more computationally expensive. Others may want
to chime in with their experiences though.

> Finally, just to be sure, the CpptrajPairDist file that is generated
> does not depend on the epsilon or minpoints that are chosen, nor the
> mask that is used in the command, correct? The clustering metric
> strictly refers to the "rms", "srmsd" or "dme" keywords?

Yes, and the metric can also be "data" to use 1 or more data sets. You
can consider the pairwise distance matrix as input to various
clustering algorithms - it is a separate entity.

> Since it produces a binary file I am not sure how to proceed if I want
> to check myself that two of these files are identical or not.

The linux 'diff' tool will tell you if two binary files are different.
There is also a description of the cpptraj pairwise distance file
format in the AmberTools 15 manual (section 29.12.1. cluster).

Hope this helps,


> Looking forward to hearing from you,
> Juan
> _______________________________________________
> 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 Fri May 08 2015 - 07:30:03 PDT
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