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

[Anton Feenstra]

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.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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