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getting the center of mass of each part of a molecule

On Monday, May 15, 2017 at 7:23:52 PM UTC-7, jeanbi... at gmail.com wrote:
> What may make this tricky is that the vinyl group can rotate at the point where it attaches to the benzene ring so the full molecule may not lie in a plane.

But the OP has coordinates for each atom which are used in the center of mass calculation for the whole molecule.  Why would the atoms be stationary for that calculation, and yet free to move in the calculation performed on a subset of the atoms?