> In addition to my previous message, I randomly chose a frame from a
> trajectory, and add this frame to the beginning of the trajectory which I
> want to align to the added first. The result is that the trajectory is not
Are you sure that the frames are not aligned? (i.e. even though they are
not at the same location in space, they are relatively aligned?) If not,
this is a problem; if they are simply translated, this is the expected
behavior (as implemented). I think the earlier ptraj versions (and maybe
even the current) translate the center of mass of the reference
coordinates to the origin (to simplify things). If this centering is
implicitly occuring (which my quick read of the code suggests), you can
overcome this by finding the center of mass (of the atom selection) for
your reference coordinates and manually translate (using the translate
command) after fitting... Alternatively, you can center .P of the
reference coordinates to the origin (in a separate ptraj run).
Otherwise, the rms() routine in rms.c would have to be modified to shift
the transformed coordinates back to the center of mass of the reference
coordinates. I have to think a bit more about (and test) the implications
of such a change, but I think it may actually be the right thing to do
here (i.e the rms code should not implicitly center to the origin but to
the center of mass of the reference coordinates) and should be a
relatively simple code change...
--tom
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Received on Fri Apr 01 2005 - 21:53:00 PST
