From: Giacomo Fiorin (
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:
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.


On Tue, May 19, 2020 at 4:02 PM Linda Sheila Medondjio <> 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