Setting up external wall is required to keep things in a compact region,
otherwise the program will collapse during the run not from restart. I
think the real problem is what Matthew described. However, I just tried
center the restart files using ptraj command given in AmberTools, but
output file does not look like a "CONFIG" file that can be read by Amber.
At least it does not contain velocity inside . Anyone knows how to center
the restart files and get an "CONFIG" file with velocity? Thanks.
On Thu, Mar 14, 2013 at 3:49 PM, M. L. Dodson <mldodson.comcast.net> wrote:
>
> On Mar 14, 2013, at 2:23 PM, R. Xiong wrote:
>
> > 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.
> >
>
> If your problem is something like water diffusing away, you can set up
> a one-sided flat well potential with a mild force constant to keep things
> in a sphere centered on some atom or point like the center of mass of
> the QM region.
>
> >
> >
> > 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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> >>>>>
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> --
> M. L. Dodson
> Business email: activesitedynamics-at-gmail-dot-com
> Personal email: mldodson-at-comcast-dot-net
> Gmail: mlesterdodson-at-gmail-dot-com
> Phone: eight_three_two-five_63-386_one
>
>
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Received on Thu Mar 14 2013 - 13:30:02 PDT
