Re: [AMBER] RMSD ptaj difficulty

From: Daniel Roe <>
Date: Mon, 5 Dec 2011 10:12:37 -0500


On Mon, Dec 5, 2011 at 1:38 AM, vaibhav dixit <> wrote:
> I looks better, but the average rmsd is still in the 40s although the
> fluctuations seems to appear in the acceptable range. Does it mean that the
> protein has moved a lot during the initial phase of MD and then stabilized
> around one structure? Is it meaningful?

Your best bet is to visualize the results of your trajectory after
centering/imaging. Instead of calculating RMSD, write the coordinates
to an output trajectory with the 'trajout' command. You don't need to
do this for the entire trajectory, just the frames where you are
getting the questionable RMSD values. For example, if your system is a
dimer or a tetramer it may be that during imaging the molecules have
become separated, which would result in high RMSD values. If this is
the case then you need to take this into account when choosing what to


Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ   08854
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Received on Mon Dec 05 2011 - 07:30:02 PST
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