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 Química 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
