Re: An outlier appear on the curve of RMSD

From: wayj86 wayj86 (wayj86_at_gmail.com)
Date: Sun Jul 26 2009 - 20:42:13 CDT

Dear Leo,

Thank you for your advice. I have visually inspected the trajectory, and
found the frame in which an outlier appeared. The protein seemed to "expand"
a bit compared with the previous frame, and was restored in the later frame.
No obvious moving could be seen. So I was wondering whether it was caused by
the random error or temporary system instability.

Best wishes,
Stanley

2009/7/25 Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu>

> Dear Stanley,
>
> On Thu, Jul 23, 2009 at 10:37 PM, wayj86 wayj86<wayj86_at_gmail.com> wrote:
> > Dear NAMD users,
> >
> > I came across a strange problem after performing equilibration with NAMD,
> > that was, an outlier appeared on the curve of RMSD. It always appeared
> at
> > the rise period of the curve, much high than the other values. For
> example,
> > If the average of the RMSD was 2.2, that it could go to more than 3.
> After
> > the outlier the curve came back to the normal state and the curve
> contained
> > only one outlier. This might happen in the calculation with cluster or
> > standalone computer and the outlier made the curve ugly. So could you
> please
> > tell me the reason? I am confused because the outlier might disappear
> when I
> > redo the equilibration again with the same conditions.
>
> Have you visually inspected the trajectory to see what happened in the
> frame corresponding to your outlier?
>
> Cheers,
> Leo
>
> > Best wishes,
> > Stanley
> >
> > --
> > The future is now!
> >
>
>
>
> --
> Leonardo Trabuco, Ph.D. candidate
> Theoretical and Computational Biophysics Group
> University of Illinois at Urbana-Champaign
>

-- 
The future is now!

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