VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue May 19 2020 - 15:12:53 CDT

Hi Linda, if you are able to get the unit cell parameters from SIESTA, you
can use the "pbc set" command provided with PBCTools:
http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
to specify the unit cell at a given frame. If you have multiple frames,
loop over them and use "pbc set -first $i -last $i", or just -allframes if
the unit cell is constant in the trajectory.

Giacomo

On Tue, May 19, 2020 at 4:02 PM Linda Sheila Medondjio <
linda.medondjio_at_icn2.cat> wrote:

> Dear VMD team,
>
>
> I would like to plot the RDF using VMD. I have generated a trajectory
> using SIESTA. The extension of the trajectory file is
>
> *.ANI. Using the ANI file I am not able to include the periodic boundary
> condition using VMD.
>
> Please how to include the PBC?
>
>
> Best Regards,
> Linda
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin