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.
hello,
thank you so much for reply. my question is why only DNA is out of the box while I have water molecules and ions in the box?
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’?