Because no *.rst generated, I cannot visualize it. So, if the maxcyc is
enough for my protein (around 500 residues), what value of ncyc I can set?
Normally, what's its range? Thanks for your suggestion again.
Best
Jason
On Fri, Sep 10, 2010 at 5:14 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
>
--
Yusheng Jason Jiang
Department of Chemistry
Georgia State University
Atlanta, 30302 GA
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Received on Fri Sep 10 2010 - 14:30:08 PDT
