Hello,

I am trying to correct PBC for a DNA system, but even after running the commands, I still see artifacts in the trajectory. Here’s what I did:

gmx trjconv -pbc whole -f traj.xtc -o step1.xtc -s topol.tpr (select system)

gmx trjconv -pbc nojump -f step1.xtc -o step2.xtc -s topol.tpr (select system)

gmx trjconv -pbc mol -center -ur compact -f step2.xtc -o final.xtc -s topol.tpr (select dna then system)

However, water molecules still appear scattered beyond the simulation box, as visible in the trajectory visualization.

Can anyone suggest how to fix the PBC issue for water molecules while maintaining a proper setup for DNA? Should I use additional options or change the sequence of commands?