> 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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Received on Tue Feb 15 2011 - 11:00:03 PST
