Thanks.
On Thu, Mar 14, 2013 at 4:45 PM, Gustavo Seabra <gustavo.seabra.gmail.com>wrote:
> 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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Received on Thu Mar 14 2013 - 14:30:02 PDT
