AMBER Archive (2003)

Subject: Re: job stopped

From: Youyi Peng (pengyo_at_UMDNJ.EDU)
Date: Thu Apr 24 2003 - 13:49:47 CDT

Thanks.
 But there is no solvent molecules included in my system. I ran vacuum MD on
unconstrainted ligand-protein complex.
 ---Youyi

"CUI, Guanglei" wrote:

> Hi,
> I've come across this problem a few times as well. In my case, it was
> because some unrestrained water molecule estrayed into the vacuum. Do
> you have solvent molecules included in your system? You can check
> your final restart file or MD snapshot and see if this's the case.
>
> cuigl
>
> On Thu, 24 Apr 2003, Youyi Peng wrote:
>
> > Hi,
> > I ran a 1 ns MD on a vacuum system in a Linux Bash shell. After 220 ps,
> > the job was stopped and
> > I found the following error message at the end of output file. I don't
> > understand what happened.
> > Please help me.
> >
> >
> > "Frac coord min, max: -0.000107843448 0.737832413
> > The system has extended beyond
> > the extent of the virtual box.
> > Restarting sander will recalculate
> > a new virtual box with 30 Angstroms
> > extra on each side, if there is a
> > restart file for this configuration.
> > EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
> > Atom out of bounds. If a restart has been written,
> > restarting should resolve the error"
> >
> > Thank you very very much!
> >
> > ----Youyi
> >
> >
>
> --
> Guanglei Cui
> Dept. of Chemistry
> SUNY at Stony Brook
> Stony Brook, NY 11790