> Is it possible to measure the rmsd of one single atom because i tried using
> ptraj and it gave me this error:
> ERROR in rms: KRMS_ reported Number of atoms less than 2
No. In fact the RMSd of a single atom (unless nofit was specified) will
always be zero. With nofit, you could simply calculate the distance the
atom has moved from the start as an indicator.
I think what you want is not the RMS deviation but the RMS fluctuations,
i.e. how much that atom is moving on average. To do this, you fit all of
the coordinates to a common reference frame and then use the atomicfluct
command.
--tec3
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Received on Tue Nov 01 2011 - 11:00:07 PDT
