From: Axel Kohlmeyer (
Date: Thu Mar 28 2019 - 11:56:12 CDT

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.


On Thu, Mar 28, 2019 at 12:43 PM Sina Zarepakzad <>

> 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.