Re: Generation of average trajectory

From: Nicholas M Glykos (
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

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,

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