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

Megha Anand meghaan... at gmail.com
Tue Oct 25 18:17:18 UTC 2016

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

Best regards,

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
> -- 
> You received this message because you are subscribed to the Google Groups 
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to cp2k+... at googlegroups.com <javascript:>.
> To post to this group, send email to c.... at googlegroups.com <javascript:>.
> Visit this group at https://groups.google.com/group/cp2k.
> For more options, visit https://groups.google.com/d/optout.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20161025/c8a7b32c/attachment.htm>

More information about the CP2K-user mailing list