VMD-L Mailing List

From: Ivan Moncayo (idmoncay_at_gmail.com)
Date: Wed Jun 15 2016 - 12:05:16 CDT

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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

> 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

>
>
>>
>> Exist a limit to the bondlist?
>>
>
> ​you will have run out of memory or address space before that limit is
> hit.​
>
> axel.
>
>
>>
>> Thanks for the help.
>>
>> --
>> Regards
>>
>> 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.
>

-- 
Saludos
Iván Moncayo R.

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