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

Q.Z. qzou at iupui.edu
Fri Oct 17 16:42:01 CEST 2003

Thanks, Anton,
 Now I have used g_cluster to get the "representative strucutre" using 
option -cl -av. It seems that the program only pick one of the many 
frames instead of generating an averaged structure. For -av option, what 
does " average iso middle structure", as written in the manual, mean? Is 
it just the median structure based on RMSD calculation? Thanks again.


Anton Feenstra wrote:

> QZ wrote:
>> 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.
> IMHO, if you are looking for a representative structure, you should be 
> looking
> at clusters. g_cluster can do that for you, it will calculate RMSD's, 
> or accept
> a matrix (.xpm format, from e.g. g_rms), and cluster low-rms pairs 
> together.
> Choosing a certain rmsd cut-off, and looking at the (middle structure 
> of the)
> largest cluster(s?) should give you insigight into what might be a 
> 'representative'
> cluster and/or structure in your simulation.

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