In my backbone rmsd plot below, there is a sudden drop in rmsd to close to zero nm at the end of the trajectory. This is the case for all my rmsd plots. I do not understand this.
Command used: gmx rms -f md.trr -s em.tpr -o rmsd.xvg
Then selected backbone for both LSQ fitting and rmsd calculation
Here em.tpr is the tpr file generated using grompp command for minimization after data collection md run.