GROMACS version:2023.2
GROMACS modification: Yes/No
I used gmx trjconv to correct for periodic boundary conditions (PBC) because the two strands of DNA separated during the simulation. I have a question: in the box containing DNA, water molecules, and ions, why was only one strand of DNA out of the box and water molecules and ions did not diffuse.
Dear @fatemeh
The box boundaries are virtual, everything diffuses around. Try something like gmx trjconv -pbc none on the whole system and you should be able to visualize the trajectory without PBCs.
All the species diffuse around, so everything - eventually - will leave the simulation box. What do you mean with ‘only DNA is out of the box’?