[gmx-users] rmsd b/w average structure and the trajectory

QZ qzou at iupui.edu
Tue Oct 14 05:06:01 CEST 2003

Dear All,
 I had a 4ns md and the simulation seems to be stable. I calculated the 
average structure using g_rmsf -ox and then looked at the rmsd between 
the averaged structrure and the frames that were used to calculate the 
average. The rmsd of the backbone is all at around 2nm. This is kind of 
way off after the average.  I was trying to get a representative 
structure for the md. Now it seems I have to pick a frame that  has the 
smallest rmsd to the average structure but at around 2nm range. I 
certainly do not feel very comfortable with that. Any suggestions?
 P.S. If the avereage works so bad, maybe we should bot bother using it. 
I have seen some disscusions on this issue before. Some suggested that 
energy minization of the average could generate a representative 
structure. How about just picking a frame when the simulation is stable 
and minimize that? Just a thought. Any input is appreciated.

Q. Zou , Ph D.
Indiana Univ.

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