visualizing geometry from * inside the box in VMD

Marcella Iannuzzi marci... at
Tue Oct 25 07:00:02 UTC 2016

Dear Megha,

what Tobias replied is correct. More information can be found, for example, 

On Tuesday, October 25, 2016 at 8:35:20 AM UTC+2, Tobias Kraemer wrote:
> 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 * file generated by CP2K. How 
>> do I see these geometry changes in * 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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