No, I was using orthorhombic box. I have run QM/MM simulations in 3ns
without any problem. And when I restart, it immediately gave me error. I
also tried if I run 3ns simulations with iwrap=0 using the same initial
configurations as used in the first run, and then restart the simulations,
there is no problem. I also visualized that the QM region is not too big
if considering periodic boundary condition.
Thanks.
On Thu, Mar 14, 2013 at 12:26 PM, Brian Radak <radak004.umn.edu> wrote:
> Are you using a non-orthorhombic box by chance? The QM region check assumes
> this, so sometimes it gives an error when there actually isn't one
> (especially with triclinic boxes).
>
> Also, have you visualized the trajectory to make sure the QM region
> actually isn't too big? Up until a few bug fixes ago the QM code would
> occasionally not SCF converge and cause "explosions". Frequently the first
> check that bombed out because of this was the QM region/box check.
> Restarting with a different random seed would almost always made this go
> away, although I haven't seen this since the bug fix.
>
> Regards,
> Brian
>
>
> On Thu, Mar 14, 2013 at 10:42 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
> >
>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for Integrative
> Proteomics Room 308
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> Department of Chemistry : Piscataway, NJ
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Received on Thu Mar 14 2013 - 11:00:06 PDT
