You are right. My QM region does have multiple unbonded molecules. I
thought there is some trick in Amber that can avoid the problem. Ok, thanks
for your suggestion.
On Thu, Mar 14, 2013 at 2:54 PM, Matthew Zwier <mczwier.gmail.com> wrote:
> Does your QM region span multiple (unbonded) molecules? If so, iwrap=1 can
> cause one molecule to wrap around the box while leaving the other in place,
> which can lead to a QM crash. (The MM routines consider nearest neighbors,
> but I've seen the QM routines not do so, or at least terminate a simulation
> before it even tries). We tend to recenter our restart files around one of
> the QM molecules to avoid this problem.
>
> Cheers,
> Matt Zwier
>
>
> On Thu, Mar 14, 2013 at 2:14 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 - 12:30:03 PDT
