Hi Brian,
Thank you for your answer.
I forgot to say that the NTP simulation about i talked about was a
production simulation in which the density is stabilized.
Also, I have tried to reduce the cutoff, but it did not have any effect on
the error.
Best regards
Gabriel
Message: 11
Date: Fri, 31 Aug 2012 10:50:06 -0400
From: Brian Radak <radak004.umn.edu>
Subject: Re: [AMBER] ERROR: max pairlist cutoff must be less than unit
cell max sphere radius!
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAJrka9x1zLCZQxnaUsVD9FcvCXE+hXO8sEV10GN93DiuedS+9Q.mail.gmail.com>
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Just a stab in the dark here. The water boxes built by leap tend to be
about 10% less dense than they "ought" to be at 300 K and 1 bar. The result
is that constant pressure runs tend to immediately contract the box about
an angstrom in all directions (although that likely depends on the size and
shape of the box). I would try a slightly bigger box or a smaller cutoff.
Regards,
Brian
On Fri, Aug 31, 2012 at 10:39 AM, Gabriel Jara <gabriel.fcq.unc.ar.gmail.com
> wrote:
> HI all,
>
> When i run a NTP simulation using pmemd.cuda (amber12 version with all the
> bugfixes applied) I have the follow error:
>
> ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
>
> When I run the same simulation, but at NTV conditions, and it works.
>
> I wonder if the bugfix.11 from Amber11 was applied to Amber12. Could it be
> the reason of the problem I had?
>
> Thanks in advance.
>
> Best regards.
>
> Gabriel
>
>
>
>
> --
> Dr. Gabriel E. Jara
> Laboratorio de Modelado Molecular
> INQUIMAE - Instituto de Qu?mica-F?sica de Materiales, Ambiente y Energ?a
> DQIAyQF - Departamento de Inorg?nica, Anal?tica y Qu?mica-F?sica
> FCEyN - Facultad de Ciencias Exactas y Naturales
> Universidad de Buenos Aires
> Intendente G?iraldes 2160 - Hall 2, 1er piso.
> Ciudad Universitaria - C1428EGA
> Buenos Aires - Argentina
> Tel: +54 11 4576 3378 /79 /80, int. 123
> ------
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Gabriel E. Jara
Laboratorio de Modelado Molecular
INQUIMAE - Instituto de Química-Física de Materiales, Ambiente y Energía
DQIAyQF - Departamento de Inorgánica, Analítica y Química-Física
FCEyN - Facultad de Ciencias Exactas y Naturales
Universidad de Buenos Aires
Intendente Güiraldes 2160 - Hall 2, 1er piso.
Ciudad Universitaria - C1428EGA
Buenos Aires - Argentina
Tel: +54 11 4576 3378 /79 /80, int. 123
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Received on Fri Aug 31 2012 - 14:00:05 PDT
