Re: Generation of average trajectory

From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Mon Oct 12 2009 - 05:06:26 CDT

> I have simulated 50 simulation trajectories of a protein unfolding
> starting from same structure, but with different seed numbers. Then I
> have clustered them according to their RMSD and Rg behavior. So for each
> cluster, I wish to look at the average trajectory, which can be looked
> as representative trajectory of that respective cluster. If I just
> average out the coordinates per timeframe, then will it be a realistic
> average trajectory representative of that set of 10 simulations? I am
> going through the literature, but I am stuck and am not able to find a
> better solution. If there is any other better and correct way of
> generating an average trajectory, please suggest.

I'm not sure what this 'average trajectory' may be. If you want an image
showing the amount of mobility encompassed by a cluster, ie. something
like this figure

http://picasaweb.google.com/lh/photo/gRLFpRvLK5Np1oQWq_VL0w?feat=directlink

then, all you need is a set of representative (superimposed) PDB files
corresponding to trajectory frames that belong to a given cluster (and,
possibly, colored according to atomic fluctuations as calculated from
the cluster).

Apologies if this is not what you had in mind.

-- 
          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, http://utopia.duth.gr/~glykos/

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