Dear user, I simulated a homodimer of 238aa each with oplsaa forcefield using gromacs-4.5.3. But while calculating the rmsf plot I got a plot in which starting and ending residue were connected by a straight line along with the actual rmsf plot. Also the two rmsf plots that it gave were slightly different from each other in few regions. I was expecting similar rmsf for both the monomers. I checked the pdb file generated after md run, it did not have chain ID but two chains were present.
Kindly let me know what is wrong with rmsf? Or what is wrong with simulation. Thanking you With Regards avya
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