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Nanotube building with a small molecules repeating unit?


#1

I have a nanotube system that is based on a heterocyclic cationic repeating unit that is ~200 MW. I would like to build and energy minimise the structure. Can this sort of thing be handled in Avagadro?
Regards
Trevor


#2

Sorry, I missed this. It’s possible, although it will depend a bit on the speed of your desktop/laptop running Avogadro.

My personal suggestion would be to build the structure in Avogadro (the main purpose) and export to minimize in LAMMPS or other force field code that can be run on a cluster.

I’ve definitely run some large polymer minimizations on my desktop, but it takes a while and at the moment, the force field code is not parallel, so it will only use one thread.