[gmx-users] Protein RMSD high

[tarak karmakar]

No, it's not at all significant in my problem as the loop is not part of
the active site, way far at the two termini. I have plotted the RMSD in
presence and absence of the loop. In absence of the loop rmsd is coming
around 0.3 nm.
Thanks Mark

Tarak


On Thu, Jun 27, 2013 at 2:37 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

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