Hello,
I have performed a minimization of a protein inside an octahedral water box. When the simulation finished I visualiced the system and the solvent box look like cubic box. I have used CHARMM36m force field. Someone can tell me why this is happening and how to fix it.
best
These kinds of questions belong in the User Discussions section, not Site Feedback.
GROMACS internally re-wraps octahedral and dodecahedral shapes. Use gmx trjconv -pbc mol -ur compact with your .tpr file to recover the octahedral shape. It’s just for visualization; there’s nothing wrong about the calculation.