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getting the center of mass of each part of a molecule

On Wednesday, May 17, 2017 at 12:14:10 AM UTC-7, Gregory Ewing wrote:
> I think the problem is ambiguous as stated. There are many planes
> you could pick through the centre of mass that divides the atoms
> into two groups. Some other rule is needed to decide which is the
> "right" one.

I took the OP at their word.  S/he wants the center of mass of the whole molecule, with the atomic coordinates as shown.  Then s/he wants the center of mass of two subsets of those atoms.  Unless I misunderstood, this isn't a particularly difficult task.