I have made a hexagonal unit cell containing a repeating piece of what I want to be a 2D nanosheet. The only big problem I am having is that the double bonds are not preserved when creating the super cell. Is there a better way to go about making 2D materials?
Hi! What is the way you want to use the final 2D structure? If it is for ab initio calculations, then you don’t need bonding info, just atom coordinates.
I am just a beginner and I am not quite sure about what ab initio calculations are. Ultimately, I would like to use the structure to do nonequilibrium molecular dynamics simulation of water permeation. Currently, I am just trying to make a molecule that I can solvate in a program like gromacs.
Well, it depends on what program you will use. If this is a classical MD, like Gromacs or Amber, you will need connectivity info. If it is quantum chemistry/physics, like VASP or SIESTA, than only atom coordinates.
At the moment, bond perception is not performed when generating a supercell.
You can save the coordinates as XYZ and re-open to re-perceive the bond orders.
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