As I’m moving from a Lennard-Jones system to a more realistic one, I need to use PMMA walls in my simulation. As I’m a tenderfoot in making such complicated molecular system, I need your advice in that regard, so:
- As far as I know I need use other packages than lammps to set up a system like a PMMA wall, and VMD is not the answer also, right? I’ve heard people use commercial packages like “Material Studio” for that which is not capable of creating PMMA at the actual density of 1.18 gr/cm^3 so after that they compress it to the desired density in LAMMP:
- Is there any open source alternative to “Material Studio” to create a system like a PMMA wall?
I’d highly appreciate it if you can refer me to any source or reading or package that I can find my way through and get my feet hardened.
This discussion might be useful for you:
Once you have a melt, you can build a wall by removing a periodic boundary, unfolding the molecules and lowering the temperature. You could alternative make a free standing melt film to avoid the removal of boundary conditions and make the wall upon cooling. That said, non of it is easy and I am not sure that a single package will provide a turnkey solution for what you want to do. Have you found the force field you want to use to model your PMMA?
Thanks for the info, about the force field actually that’s my question too. I talked to a student in another group in our department and he told me that they’ve modified a trinomer force field and use it for PMMA but I really don’t know the details at this point.
You should find out. How can you build something if you don’t know what it looks like? Look for any papers that used MD with PMMA. Are there any fully atomistic ones? Better yet, has anyone coarse grained PMMA?