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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