[CP2K-user] [CP2K:19123] Re: Query Regarding Visualization of PBC Behavior in CP2K AIMD Simulation

['SUBHASISH MALLICK' via cp2k]

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


On Tuesday, July 18, 2023 at 12:12:49 PM UTC+3 Marcella Iannuzzi wrote:

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