Re: Generation of average trajectory

From: Monika Sharma (
Date: Mon Oct 12 2009 - 09:24:16 CDT


Thank you for suggestion. This is actually different from what I asked, but
I appreciate your suggestion. It is a good way for representation.
My question was that can simple coordinates averaging per time frame for a
group of trajectories yield a meaningful average representative trajectory
for that group?

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.

For instance, the coordinate of atom 2 (R23av) of this average trajectory at
say time 3 ps be calculated as
R23av = ((R23)0 + (R23)1 +(R23)2 +(R23)3) / 4

ie sum average of atom 2 coordinates at 3ps of all the four trajectories.

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

All suggestions are welcome. If I am wrong, please correct me.

Thanking you,

On Mon, Oct 12, 2009 at 3:36 PM, Nicholas M Glykos <>wrote:

> > 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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