Re: [AMBER] increasing rmsd value

From: Siti Mohamad <>
Date: Wed, 16 Feb 2011 09:13:57 +0800

Thank you all.

Here is the rms plot for the first 100ps.

trajin 100ps.mdcrd
rms first mass out time 0.1 :1-200
center :1-200
strip :WAT
strip :Na+

On Wed, Feb 16, 2011 at 2:49 AM, Bill Ross <> wrote:

> > 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.
> You didn't send your RMS plot, so we can't see how abruptly it jumps.
> If you are including waters in your measurement, this could
> easily explain it, since waters are mobile.
> You should always fit the solute coordinates to a common set before
> getting RMS, otherwise drift and rotation will lead to an
> increase. Also, if one of a set of molecules has been translated across
> the box due to iwrap=1, you will need to use ptraj's image cmd to avoid
> and RMS jump from that.
> Bill
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(image/jpeg attachment: 100ps.jpg)

Received on Tue Feb 15 2011 - 17:30:03 PST
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