Thanks for your reply. My protein is pretty big, so I used 30000 cycles.
here is error information
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
SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
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
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
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
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
Atom out of bounds. If a restart has been written,
restarting should resolve the error
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
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
12 additional processes aborted (not shown)
Thanks
Jason
On Fri, Sep 10, 2010 at 3:32 PM, Jason Swails <jason.swails.gmail.com>wrote:
> How did it fail? Was it a linmin failure? There is a lot on the list
> about
> this. ncyc simply sets the number of "steepest descent" steps that are
> taken before conjugate gradient is started. Thus, if you are hitting a
> LINMIN failure at some point (basically, the line search can't find the
> right direction to minimize, so it backs out and retries, and after 3x it
> becomes fatal), increasing ncyc will simply make the minimization converge
> too slowly to reach the point where it failed last time (since steepest
> descent is slow to converge).
>
> If you're just trying to minimize to relieve bad contacts, you don't need
> this many cycles (30000), anyway. Thus, once you reach the linmin failure,
> your structure is fine for starting MD anyway. If you're actually looking
> for minima, then I would suggest using the xmin minimizer, which is much
> better than the built-in minimization routine. Check out ntmin=3 and the
> xmin variables in the amber manual.
>
> In the future, though, you should be more detailed about your error
> messages. I'm simply guessing at your problem here, since you didn't
> supply
> enough information regarding what went wrong.
>
> Good luck!
> Jason
>
> On Fri, Sep 10, 2010 at 3:21 PM, Jiang Yusheng <yusheng0104.gmail.com
> >wrote:
>
> > Dear all
> >
> > Here is my input file
> >
> > minimize system
> > &cntrl
> > imin=1, irest=0, maxcyc=30000, ncyc=50,
> > cut=9.0,
> > ntb=0, ntpr = 100, ntr=1
> > /
> > group input for cart restraints
> > 100.0
> > RES 32 514
> > END
> > END
> >
> > The process failed at 18100 step. Last time I did another work, and I
> > adjusted maxcyc and ncyc, the work went through.
> >
> > Here, I have a question. Is there any relationship between maxcyc and
> ncyc
> > setting? I can set randomly or I can follow some rules.
> >
> > Thanks
> >
> > Jason
> >
> >
> >
> > --
> > Yusheng Jason Jiang
> > Department of Chemistry
> > Georgia State University
> > Atlanta, 30302 GA
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Yusheng Jason Jiang
Department of Chemistry
Georgia State University
Atlanta, 30302 GA
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Received on Fri Sep 10 2010 - 14:30:03 PDT
