Query Regarding Visualization of PBC Behavior in CP2K AIMD Simulation

[SUBHASISH MALLICK]

Dear cp2k users,

I hope this email finds you well. I have a query regarding my CP2K AIMD simulation involving a water box with periodic boundary conditions (PBC) in the XY direction. Here is an excerpt from my input file:

    &CELL
      ABC 24.4797   24.4797  200.0
      ALPHA_BETA_GAMMA 90.0 90.0 90.0
      PERIODIC XY
    &END CELL

During the simulation, I expected that when a water molecule crosses the box in the +X direction, it would reappear from the -X direction due to the periodicity. However, when I visualized the trajectory using VMD, I couldn't observe this behavior. Instead, the water molecule seemed to continue in the same direction after crossing the boundary.

I would like to confirm whether this behavior is normal when using the XYZ file format or if any modifications are needed in the input file to correctly represent the periodicity.

Any insights or suggestions would be greatly appreciated.

Thank you for your time and assistance.

Best regards,
Subhasish

[Marcella Iannuzzi]

Dear Subhasish

The behaviour is correct. For visualisation purposes, wrapping into the PBC box can be applied by VMD.

Kind regards

Marcella 

[SUBHASISH MALLICK]

Dear Marcella,

Thank you for the confirmation, Can I please ask you how to apply wrapping into the PBC box by VMD?

with regards,

Subhasish

[Marcella Iannuzzi]

https://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/