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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