Border(rectangle) of the groups of the nodes affecting the position of the root node

[dilshadurrahman58]

I am trying to draw a graph using webcola which has a few groups of nodes. I am drawing the border of the groups using the technique specified here. But, the problem is my the root node of the groups is getting affected by the border of the groups. It is kind of trying to compress the layout and that is why the position of the root node is getting affected. Other nodes are doing fine. I had to drag the root to get it to its desired position. What should I do in this case?