[gmx-users] Is there any realation between structure and RMSD?

minnale minnale_gnos at rediffmail.com
Tue Oct 28 18:55:58 CET 2008

Hi all
I have simulated two systems(mutated and unmutated)of protein for 7ns and I plotted RMSD.
here my doubt is that when I see these structures(superimpose)in VMD mutated final simulated structure with respective initial one drastic changes(means helix-coil and Beta-alpha transitions) but there is no change in unmutated structure with corresponding initial one.

But when I plot RMSD, mutated structure showing low fluctuations(0.19nm)while unmutated(RMSD 0.3nm)high fluctuations.
I have mentined RMSD command like this
g_rms -f 7ns.xtc -s min.tpr -o 7ns_rmsd -pbc 
Selected c-alpha for both least square fit and RMSD calculation
What I mean to say that the structure which shows changes(coil-helix and beta-alpha)it is supposed to has RMSD high viceversa but I am getting in opposite.

Why its happening?

Any suggestions would be appreciated

Thanks in advance.
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