VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Mar 09 2015 - 03:22:53 CDT

On Mon, Mar 9, 2015 at 3:43 AM, Ondrej Marsalek
<ondrej.marsalek_at_gmail.com> wrote:
>> it *does* write out the box dimensions. but please note that VMD does
>> not store the origin of the box, so that one is reconstructed from the
>> min/max information.
>
> Oh, I see, I missed that the difference is actually the correct box
> size, thank you. Still, considering that the implicit origin in VMD
> and some file formats that do not store it is [0,0,0], wouldn't it be
> better to to use that as the lower bound?

no. LAMMPS may either discard atoms that are (too far) outside the box
or complain about inconsistent image flags.

> Would you perhaps consider a
> switch to optionally write the files like that?

that is something i have been considering, but it is not a high
priority item. the current scheme works very well and for periodic
systems, the choice of origin is arbitrary anyway.

>
> Thanks,
> Ondrej 

-- 
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.