he molecule and all the
atoms in the reference group. The center of mass of the molecules can
be used instead of a reference atom by setting <tt>-da</tt> to 0.
All atoms in the trajectory are written
to the output trajectory.<p>
trjorder can be useful for e.g. analyzing the n waters closest to a
protein.
In that case the reference group would be the protein and the group
of molecules would consist of all the water atoms. When an index group
of the first n waters is made, the ordered trajectory can be used
w