From: Sina Zarepakzad (
Date: Sat Mar 30 2019 - 05:10:34 CDT

Thanks for your reply, Dr. Kohlmeyer. So can I modify my question and ask,
is there any option in VMD - Inorganic Builder to change the orientation of
the box? I know you have mentioned that VMD has restrictions about this but
I wanted to be sure that this is one of the limitations of using Inorganic
Builder (probably for my future modeling attempts). In this case, using
lattice command is my only option for now which actually works fine for me.


On Thu, Mar 28, 2019 at 7:56 PM Axel Kohlmeyer <> wrote:

> topotools does not "create" atoms. it takes whatever atoms and positions
> are available and works with it.
> please note, that VMD in general has restrictions (as has LAMMPS for that
> matter) about the orientation of the box in space. the first cell vector
> has to be collinear with the x-axis, the second in the xy-plane and the
> third has to be placed, so there is a right handed system.
> axel.
> On Thu, Mar 28, 2019 at 12:43 PM Sina Zarepakzad <>
> wrote:
>> Hi All,
>> I am trying to create silicon (110) using VMD Topotools. I was able to
>> create atoms for silicon (100) and I am wondering if there is any command
>> that I am missing about the direction of my plane for creating (110)
>> silicon.
>> I actually created silicon (110) using lattice command in LAMMPS but
>> because I have SiO2 atomic configurations written using Topotools, I was
>> curious to learn how I can repeat this with Topotools.
>> Best,
>> Sina
> --
> Dr. Axel Kohlmeyer
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.