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

[Megha Anand]

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

[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  

[Marcella Iannuzzi]

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

[Petko Petkov]

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

===============================

 

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[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

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