[CP2K:10452] Re: Periodic boundary conditions

[Dawid das]

Thank you Matt!

Best wishes,
Dawid

2018-06-26 12:07 GMT+02:00 Matt W <mattwa... at gmail.com>:

> CP2K does not wrap molecules back into the box when writing an MD
> trajectory - so you can see the 'diffusion' of a molecule. This can be
> useful for analysis.
>
> Whether you expect molecules to diffuse that far depends on the system /
> length of simulation time. You could try running a small box of water with
> classical MD and see how that looks.
>
> As you note the molecule _is_ wrapped back into the cell when all
> calculations are done. You can safely wrap back into the cell for
> visualization etc.
>
> Matt
>
>
> On Tuesday, June 26, 2018 at 10:58:22 AM UTC+1, Dawid das wrote:
>>
>> Hi,
>>
>> I would like to repeat my question, please.
>>
>> Best wishes,
>> Dawid Grabarek
>>
>> W dniu poniedziałek, 18 czerwca 2018 10:00:14 UTC+2 użytkownik Dawid das
>> napisał:
>>>
>>> Dear CP2K Users,
>>>
>>> I am doing QM/MM MD simulation using PBC only for MM part (the QM cell
>>> is not periodic). My cell is
>>> orthorombic and I am a bit surprised as in course of simulation some
>>> water molecules drift away to vacuum
>>> when I use VMD to visualize my trajectory.
>>>
>>> Now, I am aware that if PBC work it does not matter as the image of this
>>> molecule "enters on the other side"
>>> however this visualization makes me to ask a question whether I do my
>>> setup correctly.
>>>
>>> So in course of MD what I get in XYZ trajectory file is not wrapped by
>>> CP2K and can I safely wrap those
>>> molecules/atoms later on with a script? In other words, does CP2K save
>>> only coordinates of molecules
>>> found in starting geometry but not its images as they leave the box?
>>>
>>> Best wishes,
>>> Dawid
>>>
>>> PS This is part of my input that should simply apply PBC, am I right?
>>>
>>>   &MM
>>>     &POISSON
>>>       PERIODIC XYZ
>>>       POISSON_SOLVER PERIODIC
>>>       &EWALD
>>>         EWALD_TYPE SPME
>>> !3.5/12 Angstrom
>>>         ALPHA .292
>>>         GMAX  32 32 16
>>>         EWALD_ACCURACY 1.0E-6
>>>       &END EWALD
>>>     &END POISSON
>>>   &END MM
>>>
>>>   &SUBSYS
>>>     &CELL
>>>       ABC [nm] 7.60236   6.53052   6.03591
>>>       ALPHA_BETA_GAMMA 90 90 90
>>>       PERIODIC XYZ
>>> !     SYMMETRY ORTHORHOMBIC
>>>     &END CELL
>>>
>>> --
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