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So is it a 2D or 3D simulation? I am guessing that everything is 3D because the molecular structure cannot be nicely embedded in 2D. Or is this wrong?
It is 3D simulation.
Is it possible to embed all the molecular dynamics in 2D?
What do you mean by embedding in 2d? Can you elaborate?
Is it possible to restrict the motion of the molecules to a flat surface?
It is technically possible. One 2D simulation which I can assume is graphene system. But I have not done anything similar.
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