I see. Thank you very much. I also have a problem (I feel like I have a lot of problems…haha) , which is that my ozone molecule starts out on top of the water, but after minimizing the energy, it goes into the water, and why is that
You haven’t illustrated the box vectors but perhaps you have placed the O3 “outside” of the central image such that it gets re-wrapped into the water layer. Render the box vectors and that will become apparent. Energy minimization cannot cause large-scale displacements like that so something must be incorrect about the initial coordinate file.
I see, but after the NPT step, the water molecules fill the whole box. But I wanted the water molecules to be in the lower half of the box. So Is there any way to keep the water molecules in the bottom half of the box. Thank you
If you’re applying a barostat, the void space is going to rapidly fill and the box will condense down. If you want to maintain some kind of vacuum layer, you likely need to be using an NVT ensemble.
Thank you. In fact, I have already carried out the NVT steps. So you’re saying that I can do the final simulation without adding a stress-coupled module?
Hello, I would like to ask why after adding water solvent, the middle will appear in some places blank. Why aren’t these water molecules here?
You mean in the first image? It looks like a periodic box artifact. I.e, the ozone molecules are outside the periodic box, which means that their periodic image would fill the gap.
So what can I do to replace these missing water molecules? Or is there any code that just fills the bottom half of the box with water? Thank you