Does anything look strange about the system? Very large energies, etc?
This error could be caused by the system "blowing up", i.e. a force
between 2 or more atoms becomes very large, causing the system to
expand rapidly.
Also, I noticed you're using a Langevin thermostat but not setting the
random seed (ig) - it is recommended that you use ig = -1 unless
you're specifically trying to reproduce a result.
-Dan
On Fri, Jun 22, 2012 at 9:38 AM, Elisa Frezza <elisa.frezza.gmail.com> wrote:
> Hi,
> the bugfix is applied.
> My simulation aborted at N=69.
>
> 2012/6/22 Daniel Roe <daniel.r.roe.gmail.com>
>
>> Hi,
>>
>> On Fri, Jun 22, 2012 at 9:11 AM, Elisa Frezza <elisa.frezza.gmail.com>
>> wrote:
>> > I do not run the calculation in my computer, but in a supercomputing
>> > centre, so I have to ask to them if they applied all bugfixes.
>> > I tried to do the same calculation without gpu and it seems to run.
>>
>> That makes me suspect that bugfix 12 for Amber11 was not applied:
>> http://ambermd.org/bugfixes11.html
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Lab Specialist
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-9119 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Elisa Frezza
> Ph.D. Student in Materials Science and Engineering
> Dipartimento di Scienze Chimiche
> Universitą di Padova
> via Marzolo, 1
> 35131 Padova - Italy
> Phone: +39 049 827 5149
> Skype: elisa.frezza
> Emai: elisa.frezza.gmail.com
> elisa.frezza.studenti.unipd.it
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Lab Specialist
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
_______________________________________________
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Received on Fri Jun 22 2012 - 09:00:03 PDT
