VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jun 15 2016 - 14:39:52 CDT

On Wed, Jun 15, 2016 at 1:05 PM, Ivan Moncayo <idmoncay_at_gmail.com> wrote:
> Thanks Axel for your reply,
>
>
> 2016-05-19 12:35 GMT-05:00 Axel Kohlmeyer <akohlmey_at_gmail.com>:
>>
>>
>>
>> On Thu, May 19, 2016 at 12:44 PM, Ivan Moncayo <idmoncay_at_gmail.com> wrote:
>>>
>>> Dear vmd users,
>>>
>>> I am trying to read a lammps data file with near to 600.000 atoms and
>>> more than 700.000 bonds. VMD shows an error associate to number of bonds in
>>> bondlist.
>>
>>
>> what error message is that *exactly*?
>
>
> The error message is: (are 502728 bonds and 20 bond types)
>
> atomsel: setbonds: too many bonds in bondlist: 58318 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319 58319
> 58319 58319 58319 58319 58319 58319 58319 58319
> Maximum of 12 bonds

this looks like a problem in your data file or in the way you are reading it.
you are indeed reaching a limit here, but it is not a limit of
topotools, but a limit of VMD.
your VMD binary doesn't allow a single atom to have more than 12 bonds
(that is a compile time limit and ample for all "normal" systems).

axel.

>
>
>>
>> what version of VMD and what version of topotools do you use?
>
>
> I am using version 1.9.2 (December 29, 2014), and version 1.5 of topotools
>
>>
>> and on what platform are you running?
>
>
> I am running on LINUX (ubuntu 15.10), 64 bits

>
> --
> Saludos
>
> Iván Moncayo R. 

-- 
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.