[gmx-users] Protein RMSD high

Mark Abraham mark.j.abraham at gmail.com
Thu Jun 27 11:07:51 CEST 2013

Your call. Is that motion significant to what you are trying to report
by your observation of the RMSD?


On Thu, Jun 27, 2013 at 9:03 AM, tarak karmakar <tarak20489 at gmail.com> wrote:
> 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
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