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

[Megha Anand]

Thank you so much Tobias, Marcella and Prof. Petkov!! I am now able to view 
my molecule inside the simulation box :)

Best regards,
Megha



On Tuesday, October 25, 2016 at 3:29:08 AM UTC-4, petkov wrote:
>
> 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.
>  
> Cheers,
> Petko
>  
> =============================
> 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 
> <http://computationalcatalysis.eu/Joomla_1.6.1/index.php/assis-prof-dr-petko-st-petkov>
> ===============================
>  
>
> -----Original Message-----
> From: Marcella Iannuzzi <marc... at gmail.com <javascript:>>
> To: cp2k <cp... at googlegroups.com <javascript:>>
> 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, at
> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
> regards
> Marcella
>
> 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 *-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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