VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Mar 30 2019 - 06:05:07 CDT

Any VMD plugin is subject to the same VMD limitations.

For that matter, LAMMPS has the same restrictions on the simulation box.
The lattice command is merely providing a template for placing atoms.

Axel 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.
On Sat, Mar 30, 2019, 06:10 Sina Zarepakzad <szarepakzad18_at_ku.edu.tr> wrote:
> 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.
>
> Best,
> Sina
>
> On Thu, Mar 28, 2019 at 7:56 PM Axel Kohlmeyer <akohlmey_at_gmail.com> 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 <szarepakzad18_at_ku.edu.tr>
>> 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  akohlmey_at_gmail.com  http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>