Removing PBCs as simulation prints

User discussions
1

GROMACS version: Any
GROMACS modification: No

Is there any way to use pbc for the simulation, but have the output .trr file come with pbc already removed? Or must I complete the whole simulation and then go back and process the data using gmx trjconv? It would be much more convenient for me to be able to simply remove the pbcs in real time as it prints to the .trr.

Thank you.

2

You need to use gmx trjconv after the fact. mdrun does not sacrifice performance to re-wrap things when it doesn’t matter for the physics.