I have a bunch of hydrogen molecules adsorbed on an ionic surface. The hydrogen molecules present on the surface are only the ones with angular momentum J=0 { |Mj|=0 }, and J=1 { |Mj|=0,1 }, i.e., the ground state para and ortho molecules, respectively.
Quantum mechanically they have different shapes and I want to make a distinguish between them while they are sitting on a surface like NaCl. In fact, I don't want to just indicate them simply as spheres.
How can I do that in VMD or similar softwares? Is it possible?
With regards.
For clarity's sake I would go not with different shapes but different colors, so one can immediately see the differences between these spin isomers.
I'm not sure what QM software are you using, but it should be possible to convert the geometry snapshot to a simple PDB file, but make different residue names for ortho and para H2 (e.g. OH2 and PH2). Then, you could just colour all OH2s with one color and PH2s with a different one.
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