Re: [AMBER] clustering with ptraj

From: Nhai <>
Date: Thu, 19 May 2016 20:20:13 -0400


Per 2nd step, did you remove water and ion too?

Posting exact command is very helpful too.


> On May 19, 2016, at 8:08 PM, Francesco Gentile <> wrote:
> Hello everyone,
> I am trying to perform clustering of MD trajectories using ptraj. I am
> measuring the DBI and the SSR/SST by varying the number of clusters from 1
> to 200. I tried two things that seems (at least to me) the same but I got
> completely different results:
> 1) loading the trajectories by taking a snapshot every five, removing water
> and ions, rms fitting to all the backbone atoms and then clustering in the
> same ptraj input file. This leads to an optimal value (by combining a DBI
> local minimum and the elbow criterion to the ratio) of 116 cluster.
> 2) loading the trajectories with a snapshot every 5, rms fitting and
> writing out a fitted trajectory in one file. Loading the fitted one and
> clustering in another one. This save of course time but gives a different
> result, with DBI values exceptionally low (starting at 0.15 and going down
> to 0.06 in the minimum).
> Does anyone have a clue about that? I though that both methods were the
> same but it seems like it is not like this. Best regards
> --
> Francesco Gentile
> PhD Student, Biophysics
> CCIS 3-215, Department of Physics
> 7-112, Li Ka Shing Centre for Health Research Innovation
> University of Alberta, Edmonton, AB T6G 2E1
> Canada
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Received on Thu May 19 2016 - 17:30:05 PDT
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