Periodic boundary conditions

[Dawid das]

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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