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 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Fri Aug 31 2012 - 08:00:05 PDT
