I typically just leave it at its default. Take a look at your mdout file
and see about how many steps you have to run to reduce the bad contacts
(check the gradients).
Good luck!
Jason
On Fri, Sep 10, 2010 at 5:19 PM, Jiang Yusheng <yusheng0104.gmail.com>wrote:
> 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
> _______________________________________________
> 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
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Received on Fri Sep 10 2010 - 15:00:04 PDT
