An outlier appear on the curve of RMSD

From: wayj86 wayj86 (
Date: Thu Jul 23 2009 - 22:37:04 CDT

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.

Best wishes,

The future is now!

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