[gmx-users] RMSD

[minnale]

Hi users, 
   I have run two systems of protein simulation for 7ns, the difference between these systems change in the few resdues. After that I have done  RMSD analysis.
When I superimposed these two 7ns protein simulation systems with crystal structure seperately,I noticed that in one system no change in simulated structure with to the crystal struture say "A" . But in another system lot of changes in simulated structure compare to the crystal structure say "B".

1.RMSD:
       When I plot RMSD
g_rms -f prot7ns.xtc -s intial.tpr -pbc -o prot_7nsrmsd, similar command for aonther system also but files will be differ.

The A structure has high RMSD values rather than B.

Could you tell me please why its happening? am I done wrong anywhere my simulation? 

I think if any structure doesnt undergo much conformational changes it has to show low RMSD values, I am getting quite opposite. am I right?

Thanks in advance.
         
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