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?