AMBER Archive (2005)

Subject: RE: AMBER: Sander bomb - atom out of bounds

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Apr 21 2005 - 13:02:18 CDT

Dear Joseph,

> While attempting a first minimization run in a 10
> Angstrom box, the

> following error was encountered:
>
> >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.
> >SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
> >Atom out of bounds. If a restart has been written,
> >restarting should resolve the error

Did you really do minimisation? Or do you mean equilibration with MD. If
this has happened during minimisation then there is something very wrong
with your system as an atom (or more) have flown a great distance. If we
could see the beginning few steps from your output it would be easier to
diagnose. Check for things like very large VDW terms etc which indicate you
atoms too close together.

If you were doing MD then this error can occur occasionally but only after a
very long run (ns or more) generally. Take a look at your mdcrd file from
your md and see if anything is wrong.

If all seems fine with the MD then try setting nscm=1000 or so to remove
centre of mass velocity. Also you could restart you simulation from the
restrt file as suggested in the error message. Only do this, however, if you
are convinced your simulation is okay.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

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