VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jan 01 2019 - 22:55:07 CST

On Tue, Jan 1, 2019 at 4:18 AM HEMANTH H 18310019 <hemanth.h_at_iitgn.ac.in> wrote:
>
> Dear all,
>
> I have a water box that has a hexagonal unit cell. The Radial distribution function plugin shows an error "only orthorhombic boxes supported". Kindly advice me as to what can be done to calculate gofr in such a system.

you have multiple options:
- transform your trajectory into a supercell (i.e. make periodic
copies until you can wrap this without disrupting the structure into
an orthorhombic cell).
- modify the VMD source code, so that the limitation to orthorhombic
cells is lifted
- find a tool, that can handle computing g(r)s for non-orthogonal cells
- program such a tool for yourself, which may be easier than modifying VMD

axel.

>
> --
> Hemanth H 18310019
> Research Scholar
> IIT Gandhinagar 

-- 
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.