visualizing geometry from *-pos-1.xyz inside the box in VMD

[Tobias Kraemer]

Dear Megha,


the pos file doesn't contain any information about the simulation box. 
However, you can tell VMD manually what the parameters are. Open the 
terminal (Externsions/Tk Console) and type pbc set {a b c alpha beta gamma} 
<enter> pbc box_draw.
This should yield the desired result, i.e. the simulation box / unit cell 
of lengths a b c and angles alpha beta gamma. I suspect in your case the 
cell will be a simple cube of side length a Angstrom. I am not entirely 
sure, but I suspect that the box will only be drawn for one frame of the 
trajectory, but I don't know if there is a way to fix the box for all 
frames. At least for a first visual inspection this should be sufficient.

Hope this helps

Tobias  

     

On Tuesday, October 25, 2016 at 1:57:29 AM UTC+1, Megha Anand wrote:
>
> Dear CP2K users,
>
> Forgive me for asking several trivial questions. I am still new to CP2K. 
> Many thanks to several members of this group because of whom I am able to 
> take baby steps towards learning this powerful program.
>
> I am using VMD to visualize the *-pos-1.xyz file generated by CP2K. How 
> do I see these geometry changes in *-pos-1.xyz file inside the simulation 
> box. Is there a keyword that allows to print these coordinates inside the 
> simulation box for each geometry optimization step. I am doing a 
> non-periodic computation on a diatomic system using MT poisson solver and 
> would like to get a feel for the spacing between the system and then cell 
> walls.
>
> Thank you so much for your time and help!
>
> Best regards,
> Megha
>
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