Re: [AMBER] increasing rmsd value

From: Fredrick Devadoss <>
Date: Tue, 15 Feb 2011 14:17:52 +0100

Hi Siti,

It seems that you haven't align all the structures. Align all the structures and then calculate RMSD.
I hope this will work-out.


On Tuesday, February 15, 2011 14:07 CET, Siti Mohamad <> wrote:
> Dear Amber,
> I've run 2ns simulation and plotted the potential energy and volume from
> the output file. They looked stable, however when I did the rmsd analysis
> on the system referring to the first frame of the trajectory, the rmsd
> values increasing from 0.2 A up to more than 100 A.
> Is this possible?
> thanks
> Regards,
> Siti

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Received on Tue Feb 15 2011 - 05:30:05 PST
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