Hi all,
I have tried to research this question, only to result in more questions.
I have recently been reading about nanopatterning of amorphous silica, polymers, etc. (I have also previously posted a question on this.)
Now it seems to me that many people, almost too many, prepare these nano patterns by deleting atoms out of their regions resulting in the desired shape.
This seems hardly a proper way to prepare a simulation, especially if amorphous. I mean there is no guarantee of the stability of the resulting structure or that it will be representative or even physical. (think of a complicated polymer chain chopped up by this deletion, or an imbalance of charges resulting from it)
My question to the lammps communitiy is, from an MD prespective, is that at all a good way to consider for such problems? So far in my readings VMD scripting has been used for cystalline solids, resulting in beautifully finished nano patterns. But that's largely due to the simplicity of those structures. I mean it's easy not to end up with half a benzene ring and some carbonyls flying around if the polymer is crystalline.
I have tried out some imprinting procedure (that was my older question) but to no avail. This is next on my to do list and if anyone has done this I'd appreciate the insight.
H