Is anything weird happening when you visualize it? It's also likely that
only a couple hundred, or maybe a thousand or so, steps will be sufficient
to relieve bad contacts. You can check the gradient information to be sure.
Good luck!
Jason
On Fri, Sep 10, 2010 at 5:10 PM, Jiang Yusheng <yusheng0104.gmail.com>wrote:
> 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
> _______________________________________________
> 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
Received on Fri Sep 10 2010 - 14:30:06 PDT
