Hi AMBER folks,
I have some questions about the output of the diffusion option
in ptraj.
First, I presume that the columns signify different atoms,
but for some reason the number of columns is different than
the number of atoms in the mask (408 instead of 553, e.g.)
when I open the .xmgr file in SigmaPlot.
Second, there seem to always be some strange errors at the very
end of the trajectory - at least so it seems in SigmaPlot. It
looks like there are multiple numbers in each cell, for the last
10 snapshots or so.
Finally, is there some documentation that describes exactly what
is being calculated in the output files? The description in the
manual isn't very clear: what does "average mean square displacement"
mean - average over what? Mean over what?
Thank you in advance,
Dmitry.
Received on Thu Jul 12 2001 - 11:32:38 PDT
