[CP2K-user] [CP2K:19121] Query Regarding Visualization of PBC Behavior in CP2K AIMD Simulation

'SUBHASISH MALLICK' via cp2k cp2k at googlegroups.com
Tue Jul 18 09:04:03 UTC 2023

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,

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