Re: [AMBER] clustering analysis changes my coordinates

From: Daniel Roe <>
Date: Fri, 23 Jul 2010 10:46:04 -0400

Someone more knowledgeable about clustering in Ptraj may want to chime
in here, but I suspect that you're using 'rms' as your distance
metric, and I the RMS functionality in ptraj does indeed change around
coordinates during the course of the RMSD calculation (that is to say
inside the function itself). So I don't think this can be prevented.
Maybe you could realign the frames after clustering?

On Thu, Jul 22, 2010 at 9:55 PM, Geoffrey Wood <> wrote:
> Dear Amber Community.
> I have been doing some clustering analysis recently and was surprised to see that after ptraj performed the clustering the coordinates of the trajectory have changed.  This is important to me because before the clustering was done I had aligned  all the frames to 3 atomic centers ('mask1') and then performed the clustering on another part  of the molecule ('mask2').  So before the clustering is done these atoms are aligned, after the clustering is done none of the clusters have these atoms aligned.
> Is there anyway for this to be prevented?
> Thanks in advance,  Geoff
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Received on Fri Jul 23 2010 - 08:00:05 PDT
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