Re: Generation of average trajectory

From: Nicholas M Glykos (
Date: Mon Oct 12 2009 - 12:55:11 CDT

Hi Monika,

> Reframing the question, if we have 4 multiple trajectories 1, 2, 3 and 4.
> So, Is a trajectory generated as average of coordinates
> Rij = (Rij0 + Rij1 + Rij2 + Rij3) / 4
> be called as representative trajectory of that group , where i is atom
> number and j is the frame number.

Ok. I see where you are getting at, but probably this sort of averaging is
not what you want: since the trajectories have independent histories
(though the structures belong to the same cluster), there is no
justifiable reason for averaging the structures that belong to the frames
that happened to have the same index (to make this clear, why
averaging the structures on frame 136 and not, for example, the one on 123
with those on 153, 148 and 161 ? These two choices are equally arbitrary).

> And also if I can use this average trajectory for further PCA analysis,
> will it be meaningful?

For PCA-based analysis (both cartesian and dihedral) you can merge the
trajectories using catdcd, identify clusters in the merged trajectory,
(possibly) construct a DCD file containing all structures that belong to a
specific cluster (keeping in mind that such a DCD file would no longer be
a trajectory of anything), analyse your clusters with your favorite tools.


          Dr Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615,

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