VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Oct 02 2019 - 10:28:54 CDT

You need to use "pbc box -center origin" :-)

https://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

On Wed, Oct 2, 2019 at 11:18 AM Madhur Aggarwal <
madhur.aggarwal_at_research.iiit.ac.in> wrote:

> Hi all,
>
> I am beginner in VMD. I have a lammps data file which contains the
> dimensions of my simulation box. I want to translate my system to the
> center of the box. It would be great if someone could help me in figuring
> out how to do it.
> Also, in my lammps data file, my simulation box dimensions are:
>
> -10.000 10.000 xlo xhi
> -10.000 10.000 ylo yhi
> -10.000 10.000 zlo zhi
>
> So VMD origin should be at the center of my simulation box, which is not
> the case when I visualize it by using "pbc box" command. I am not sure why
> this is happening.
>
> Thanks in advance,
> Madhur Aggarwal
> 

-- 
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