I am doing NPT simulation (
fix npt ) of Polymer in electrolytes.
I want to create a vacuum at the bottom of the simulation box and all atoms cannot go into. The situation is shown in the figure. What is the best way of doing this? If I do not use a vacuum, and use a “
fix wall” and “
boundary p p f” to build a wall at the two faces of Z-axis, could the Cl- ions at the bottom still interact with the Na+ ions at the top?
I want to use a vacuum because if I apply electric field along Z-axis, ions will be driven to the top or bottom of the box and they will not cross the boundary. The polymer is at the bottom of the box by using “
By the way, if there is no vacuum and when electric field is used along Z-axis, will ions gather into the bottom and top of the box?
I mean, although there is an electric field pushing positive ions (Na+) up and negative ions (Cl-) down. But because of periodic boundary conditions, the Na+ ions and Cl- ions are getting closer and will eventually cross the Z boundary. Is this interpretation correct or wrong?
Thank you in advance for checking this topic.
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