[CP2K-user] [CP2K:19122] Re: Query Regarding Visualization of PBC Behavior in CP2K AIMD Simulation

Marcella Iannuzzi marci.akira at gmail.com
Tue Jul 18 09:12:49 UTC 2023

Dear Subhasish

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

On Tuesday, July 18, 2023 at 11:04:04 AM UTC+2 SUBHASISH MALLICK wrote:

> 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

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