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Talk:Mod:Hunt Research Group/VMDindexing

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When visualising things in VMD it is necessary to know that VMD starts reading the file calling the first atom, atom 0.

If you use the index number from VMD and apply it to another file, you will be looking at a different atom, unless that file also starts from atom 0 (unlikely).

For .xyz files generated from MolClsuter or ChemShell files this means that atoms numbers in VMD are on less than in the opt.chm files.

Also when using VMD to visualise MD trajectories, this will also apply. If you want to exchange one atom for another type, changing the metal at the centre of a catalyst for example, you will need to add one to the index number from VMD to change the atom you intended to change.