Hi Dan,
thanks for your reply.
So I tried using the sieve option, and I got the same thing: all frames in one cluster. I tried using epsilon (2.3) instead of cluster count and then it created ~200 representative pdb's!
Yes, I read the paper you're mentioning back in the day. I'll have to read it again and try some other method, as the average linking isn't making much sense for me. Any suggestions on what to try first?
Thanks very much,
Amparo
Amparo Garcia-Lopez, Ph.D.
Pharmaceutical Biochemistry
School of Pharmaceutical Sciences
University of Geneva
Quai Ernest-Ansermet 30
1211 Genève 4 - Switzerland
Tel: +41 (0)22 379 3376
Fax: +41 (0)22 379 3360
e-mail: Amparo.GarciaLopez.unige.ch
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: 15 April 2013 16:09
To: AMBER Mailing List
Subject: Re: [AMBER] clustering places all frames in one cluster
Hi,
On Mon, Apr 15, 2013 at 2:26 AM, Amparo Garcia Lopez
<Amparo.GarciaLopez.unige.ch> wrote:
> what I get is 10 clusters in which, 19,991 frames are in the first cluster (c0), and the rest of the clusters have only one point in them.
>
> This is not possible, I've done clustering of this RNA before using diff settings (e.g., collecting 1 frame every 100 instead of every 20) and I get clusters with nicely distributed occurences.
> what do you think I have done wrong? Maybe 10 clusters is too much, maybe collecting 1 every 20 is not a good idea? We are talking about a trajectory of 400 ns here.
Clustering is very much an art form; there really is no
one-size-fits-all procedure for clustering every trajectory. Settings
that work well on one system may give poor results on another (as you
have seen). Have you tried varying epsilon instead of cluster count,
or trying some of the other clustering algorithms available in ptraj?
You can also try the 'sieve' option, which will first cluster on a
reduced set (similar to the offset method) then add frames back in
based on similarity to cluster centroids. If you haven't yet, I highly
recommend you read through the clustering journal article from Shao &
Cheatham et al., JCTC (2007) v 3 p 2312-2334.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Apr 19 2013 - 01:30:02 PDT
