However, in the final simulation results (taking CV = 9.0 Å as an example), some water molecules escape beyond the cell boundaries defined in my input file. To address this, I applied a wrapping operation to the atomic/molecular positions in the output pos.xyz file, bringing the out-of-cell atoms/molecules back into the cell using periodic boundary conditions. Then, I recalculated the CV for each image in the trajectory. Surprisingly, after wrapping all atoms/molecules periodically, the CV is no longer the initial value (9.0 Å), but instead takes on different values. However, if I skip the wrapping operation, the CV remains at the initial value of 9.0 Å. It seems that the CV definition does not account for periodicity during the simulation.
I would like to ask whether CP2K has this issue, or if there might be other reasons causing this problem in my simulation results.
If someone have time to give me some advice, I would appreciate it.
Best regards