[gmx-users] Protein RMSD high

[tarak karmakar]

Dear All,

While simulating a protein, I see the rmsd fluctuates around a mean of 0.6
nm. I carefully looked at the trajectory (VMD movie) and saw there are two
flexible terminii fluctuating with a very high amplitude contributing to
the high value of RMSD. Is it ok to report this problem with this RMSD
value?

Thanks
Tarak