VMD-L Mailing List

From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Wed Oct 02 2019 - 11:18:32 CDT

Hi Madhur,

# select atoms in your system
set all [atomselect top all]

# find the geometric center of the atoms
measure center $all
> x y z (assume these values are not 0)

# move your system to the center (0,0,0)
$all moveby {-x -y -z}

That should do it.

Bassam

On Wed, Oct 2, 2019 at 8:55 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
>