Re: [AMBER] RMSD value

From: Daniel Roe <>
Date: Sun, 18 Dec 2011 09:27:03 -0500


If your system is periodic then it's possible this is from an imaging
issue. If that is the case you could center on your solute and
re-image. Have you tried visualizing those frames of the trajectory to
see what is happening?


On Sat, Dec 17, 2011 at 4:40 PM, Esam Tolba <> wrote:
> I ran a simulation and from it I calculated RMSD. And all the values of
> RMSD is flactuated from 0.9 to 2 but in fiive frames in the middle of the
> simulation the value of RMSD jumped to 17. does anybody know what could be
> the reason of that?
> *Best *
> *Esam*
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ   08854
AMBER mailing list
Received on Sun Dec 18 2011 - 06:30:04 PST
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