Re: [AMBER] How to do clustering analysis by ptraj?

From: Thomas Cheatham <>
Date: Tue, 17 Sep 2013 10:50:49 -0600 (Mountain Daylight Time)

> trajin ../remd.340.8k.binpos
> cluster out cluster all Amber representative pdb average pdb averagelinkage
> epsilon 3.0 rms :2-103.CA
> I finished the ptraj cluster analysis, use the above input file.
> The whole process is used about 20 days.

As is often mentioned on this list, it is wise to start with small /
tractable problems first before jumping into a 20 day potential waste of

First, it is advisable to understand how many potential clusters might be
present and/or to start with a smaller trajectory. Normally you only
initially want to look at ~1000-2000 frames in order to make the
calculation tractable.

I often will create a 2D-rms plot (with 2drms in ptraj or rms2d in
cpptraj). For cpptraj, assuming I have a file with 1 million frames, I
would load every 1000th,

trajin mdcrd 1 999999 1000
rms2d out 2drms.gnu :2-103.CA

Then look at it with gnuplot.

> ( *Why spend so long time ?*)

You had lots of frames and it is a comparison of every frame to every
frame so the complexity grows rapidly...

> cluster.txt

That file (cluster.txt) should have information on the cluster
populations. There are also in the log file.

I do not know why it is not able to write the files, but perhaps the disk
was full? Note that in general likely you do not want 5476 clusters as
they would be very difficult to look at / analyze (unless doing some kind
of Markov state model). Rather than cluster by epsilon, initially, I
would try to specify some reasonable set, something like 10 or 25
clusters. I would also use the sieve option so that it would be much
faster. With 32500 frames, I would do every 25th frame,

cluster out cluster-10 all amber representative pdb average pdb \
  averagelinkage clusters 10 rms :2-103.CA sieve 25

Note also that there are new and faster cluster commands in cpptraj...


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Received on Tue Sep 17 2013 - 10:00:02 PDT
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