VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri May 19 2017 - 19:40:24 CDT

On Fri, May 19, 2017 at 7:52 PM, Arthur Oliveira Vale <
arthurovale_at_uchicago.edu> wrote:

> Dear All,
>
> I'm running a hexagonal membrane system and would like to set up the
> vectors for the periodic images so that they correctly match the sides.
> I've tried doing the following:
>
> pbc set {123 0 0 60 90 90}
>
> where 123 is the desired size for the vector. Despite that, vmd displays
> the periodic images as if the alpha angle was set to 90. I've tried
> changing the alpha angle directly with "molinfo top set alpha $alpha" where
> $alpha is some angle, and no matter what angle I choose for $alpha my
> images are the same. Would anyone know why "molinfo top set alpha x" is not
> working? Also, how can I set the periodic vectors for a hexagonal system?
>

​pbc set takes the length of the three box vectors and the three angles as
argument. so {123 0 0 60 90 90} is illegal input.

since you cannot provide the box as vectors, your system has to follow
certain conventions:
- the a vector has to be collinear with the x-axis
- the b vector has to be in the x-y-plane
- the c vector has to be oriented to form a right-handed system

periodic display of non-orthogonal systems will only be correct, if your
geometry follows these conventions.

axel.
​

>
> Thank you in advance,
>
> Arthur Vale
> 

-- 
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.