> I would like to be sure if the 'average' command of ptraj is just a simple
> average of coordinates of the masked atoms, or if there is any implicit
> previous transformation, like removing the translation of the the center of
> mass for every frame.
ptraj performs a straight coordinate average; so, for example, if your
molecule is rotating quickly, the average will come out to a blob or
point. For the average to be meaningful, normally you have to put the
trajectory snapshots into a common reference frame. This can be done by
RMS fitting the region of interest... --tec3
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Received on Sat Feb 20 2010 - 01:30:03 PST
