[CP2K-user] [CP2K:19124] Re: Query Regarding Visualization of PBC Behavior in CP2K AIMD Simulation

[Marcella Iannuzzi]

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


On Tuesday, July 18, 2023 at 11:57:03 AM UTC+2 SUBHASISH MALLICK wrote:

> 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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