Hello everyone,

In my previous molecular dynamics simulations using GROMACS, I used a dodecahedral box for the PDE5 (phosphodiesterase) protein. For a new system involving the FimH adhesion protein, I’ve opted for a cubic box.

This made me wonder: What are the criteria or best practices for choosing between a cubic and dodecahedral box for protein systems?

Are there specific structural or computational factors to consider—such as protein shape, size, or orientation—that help in making this decision? I’d appreciate any insights, especially from those who have worked on globular versus elongated or membrane-associated proteins.

Thanks in advance!