If I had to guess, I'd guess that you have a QM region such that
(QM size + cutoff) > (0.5 * box side),
such that in periodic boundary calculations the QM region can see its
image, which is not allowed in Amber. However, this should be independent
of iwrap: it would appear anytime you try o use periodic boundary
conditions.
Could you reproduce the actual message here? That would make the guessing
lot easier.
Gustavo Seabra
Professor Adjunto
Departamento de Qu�mica Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7450
On Thu, Mar 14, 2013 at 11:42 AM, R. Xiong <rchxiong.gmail.com> wrote:
> I am running QM/MM simulations using Amber with iwrap=1. It was running
> successfully, but when I restart the program, the program crashes because
> of QM/MM region is too large. I believe this should be caused by iwrap
> option. If iwrap=0, this problem will disappear, but my question is that if
> there is any way to deal with the problem when still using iwrap=1.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 14 2013 - 11:00:02 PDT
