VertexCoordinates
is usable in Graph3D[]
:
pts = Flatten[PadRight[{{0, 0}, {1, 0}}, {2, 3}, #] & /@ Range[0, 9], 1];
Graph3D[EdgeList[GridGraph[{2, 10}]], VertexCoordinates -> pts]
However, if you insist on using GraphPlot3D[]
, the correct option to use is VertexCoordinateRules
:
GraphPlot3D[GridGraph[{2, 10}],
VertexCoordinateRules -> MapIndexed[First[#2] -> #1 &, pts]]