AMBER Archive (2003)

Subject: Re: job stopped

From: CUI, Guanglei (cuigl_at_morita.chem.sunysb.edu)
Date: Thu Apr 24 2003 - 13:06:25 CDT

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