What are the simulation conditions to perform a MD simulation in nano-scale e. g. graphene nanoribbons or semiconductor nano-particles. I mean what would be the simulation box domain? Should the simulation box be greater than the nano-structure under consideration or can the simulation box be filled up? What about periodic boundary condition?
With MD you have to consider Boundary Conditions. The simulation box should be larger enough than the nano-structure under consideration of course. You have to specify an R cut value for your potential beyond which the interactions are negligible. For example your R cut times two should be less than the cell length, I mean the computational cell ( 2*Rcut
If you want to study an isolated nano particle by MD, you actually don't care of the box and of course use free boundary conditions. I hope that helps.
Answer to your question depends on what you are looking for in MD simulation. If you want to analyse a free nano particle in vacuum (like its geometry and phase transitions due to temperature or size dependent properties like surface energy or dipole moment) so you just turn off PBC and do simulation in gas phase (vacuum). But if you want to apply pressure on the nano particle so you need to consider PBC (This is not easy as you don't want periodic images to interact so you have to introduce a pressure inducing medium like solvent.). If you want to simulate the nano particle interactions you have two options:1) consider two nano particle in specified distances in vacuum (feasible)or 2) consider a box with number of particles and use PBC (limitation on size of the nano particles.).
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