VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Apr 04 2015 - 22:51:09 CDT

On Sat, Apr 4, 2015 at 10:46 PM, Benjamin Cowen <bjcowen90_at_gmail.com> wrote:
> May I ask a question about Topotools?
>
> When generating lammps data file from xyz format per say, the box bounds are
> -0.5 to 0.5 for all dimensions, yet my atomic coordinates go up much higher
> than this. All I am doing is loading in xyz file into VMD, opening up
> TKconsole, and then doing:
>
> topo writelammpsdata SiC.lmp
>
> Everything else looks fine with the data file except for the box bounds.

how should topotools (or rather VMD) know?
an xyz file has no information about the box dimensions, thus
topotools just uses some dummy values that, as you have noticed, are
obviously bogus.

axel

>
> Best Regards,
>
> Ben 

-- 
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.