Your problem seems to be a combination of two factors:
1. Differently from the MM part, the neighbor list of the QM part contains
*any* atom that falls within cutoff of *any* QM atom. All the QM atoms
share the same neighbor list.
2. Having unbound molecules can make one of them diffuse and, using inwrap,
it may be falling too far from the other QM atoms. As a result, the "QM
region" now is way too large, and you see the error message. Yo can easily
verify that by printing the Qm region (look for the writepdb QM option in
the Amber manual.
The solution would be, first, trying to restrain the water so it doesn't go
that far, as was suggested by Bud, or recenter the file and redefine the QM
region, as suggested by Matt. But keep in mind that, if the error comes
back again, it may also be necessary to increase the size of your box.
Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7450
On Thu, Mar 14, 2013 at 3:14 PM, R. Xiong <rchxiong.gmail.com> wrote:
> Yes, that was the message. So I just got lucky by using iwrap=0? No way to
> solve this problem? Thanks.
>
>
> On Thu, Mar 14, 2013 at 1:29 PM, Gustavo Seabra <gustavo.seabra.gmail.com
> >wrote:
>
> > 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.
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> > >
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Received on Thu Mar 14 2013 - 14:00:03 PDT
