Generation of average trajectory

From: mon_sharma_at_research.iiit.ac.in
Date: Mon Oct 12 2009 - 02:26:02 CDT

Hello All,

I have a basic question regarding generating an average trajectory.

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.

Thanking you,

Regards
Monika
 

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