Re: [AMBER] Questions on Minimization

From: Kevin Hauser <84hauser.gmail.com>
Date: Fri, 10 Sep 2010 17:13:03 -0400

Hi, Jason,


If your goal is to equilibrate the protein, more minimization isn't going to
be the ideal procedure. Is equilibration your goal, or is there something
specific that only this procedure will do for you?


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
>



-- 
-- - -
HK
-------------------------------------------------------
Kevin Eduard Hauser
National Science Foundation,
LSAMP Bridge to the Doctorate Fellow
The Department of Chemistry
Stony Brook University
Stony Brook, New York 11794
Phone: (561) 635.1848
Email:  84hauser.gmail.com
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Received on Fri Sep 10 2010 - 14:30:05 PDT
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