I’m carrying out a project to simulate gold nanorods and study a particular feature. It’s the first of this kind I’ve done. I have decided to build and equilibrate a single seed as opposed to an ensemble but I wonder if that’s the right choice.
Would it be appropriate to treat the rod with periodic boundary conditions, so a small region represents an infinite rod? Some simulation methods/codes allow you to set a periodic boundary in certain directions and open boundary in others.
Alternatively you might like to check the convergence of a property against rods of various lengths.
Is this “seed” the whole structure, or a local feature/defect attached to the nanorod?
Thanks and sorry for the really late reply. The seed is the whole structure for now.
I would suggest choosing initial simulation parameters based on bulk gold and and isolated adsorbate (if there is one), then primarily working with periodic rods so you can get sensible metallic conductivity along the rod direction. Then you need to converge the length to reduce image interaction effects - or gather enough information to extrapolate to an infinite rod.
A lot of the practicalities depend on your underlying simulation method, ASE can handle all these scenarios.