Re: [AMBER] clustering in ptraj

From: Daniel Roe <>
Date: Mon, 9 Mar 2015 08:12:25 -0600


Clustering tends to be more of an art form than a science, and it can
be difficult to tell a prior what algorithm/distance metric/clustering
parameters will give you optimal clusters. Usually something like
hierarchical average-linkage or K-means with RMS give decent results,
but it's not guaranteed. I highly recommend reading this article on
clustering MD trajectories by Shao & Cheatham III et al.:


On Mon, Mar 9, 2015 at 12:48 AM, Mary Varughese <> wrote:
> Sir,
> I read that there are different options to perform clustering in ptraj.
> It would be helpful if you could give some suggestions on my problem.
> I have a nucleic acid system which is a modelled one. have run a 50 ns
> simulation (explicit).
> obviously the starting structure may be some different from the probable
> structure.
> Which clustering algorithm do you think is suitable under such situation.
> thanking you
> Mary Varughese
> _______________________________________________
> 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)
AMBER mailing list
Received on Mon Mar 09 2015 - 07:30:10 PDT
Custom Search