[CP2K:8295] Re: visualizing geometry from *-pos-1.xyz inside the box in VMD

Petko Petkov oh... at chem.uni-sofia.bg
Tue Oct 25 07:28:55 UTC 2016

Dear  Megha, if you want to apply the cell parameters for all frames in your 
trajectory, just go to the VMD Main menu -> Extensions -> Analysis-> Radial 
Pair distribution function, in the new opened window "Radial Pair 
distribution function" on the upper left corner click on the Utilities menu 
and choose cell parameters, here enter your cell parameters.



Assist. Prof. Dr. Petko St. Petkov  

Faculty of Chemistry and Pharmacy 

University of Sofia  

1126 Sofia, Bulgaria  

tel: +359 2 8161 433

website: http://computationalcatalysis.eu 


-----Original Message-----

From: Marcella Iannuzzi <marci... at gmail.com>

To: cp2k <cp... at googlegroups.com>

Date: Tue, 25 Oct 2016 00:00:02 -0700 (PDT)

Subject: [CP2K:8295] Re: visualizing geometry from *-pos-1.xyz inside the 
box in VMD

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


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 [http://pos-1.xyz/] file 
generated by CP2K. How do I see these geometry changes in *-pos-1.xyz 
[http://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,


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