Hello,
I’m currently working on simulating the L-L extraction system and require some guidance regarding my simulation setup.
I’ve patched the organic solvent box, containing ligands, with the aqueous phase containing ions along the z direction. However, I’m uncertain about the appropriate approach for analysis. Specifically, I’m unsure whether it would be okay to assume the formation of three interfaces (top, center, and bottom) considering periodic boundary conditions (PBC).
Alternatively, I’m considering using walls at z=0 and z=box-z to focus solely on studying one interface (at center). However, I’ve come across some discussions discouraging the use of walls due to potential complications or biases introduced into the simulation.
- Is it acceptable to analyze the system assuming the presence of three interfaces under PBC?
- Should I opt for using walls at z=0 and z=box-z to study just one interface? Are there any significant drawbacks associated with this approach?
I attempted to elongate the box in the z direction (as an alternative to using walls approach) after a short NPT equilibration run (2 ns) to create vacuum along z. However, the box collapsed to its original dimensions during the NVE (post the NPT equilibration stage).
- Are there any other approaches we can employ to focus solely on the center interface without introducing walls?