made SHAKE work again with particle decompostion

made SHAKE work again with particle decompostion

Making a graph not starting at atom zero was not allowed,
as this did not properly with shifting atoms (and was never
called that way for shifting), but SHAKE with PD requires this.
Now also shifting not starting at 0 works correctly.

Change-Id: Icfbf51db36f2dfd7c76ea7e4e2a4bb4b0b895e47