Dear Jason,
Is ncyc > 100 better? I'm currently running ncyc=500, maxcyc=1000
Best,
Brandon
On Wed, Jun 27, 2012 at 10:59 PM, Jason Swails <jason.swails.gmail.com>wrote:
> I would also suggest setting ncyc ~ 100 or so -- conjugate gradient
> minimization tends to misbehave for highly strained structures, so you may
> want to use more steepest descent steps to get to a better structure.
>
> HTH,
> Jason
>
> On Wed, Jun 27, 2012 at 8:44 PM, case <case.biomaps.rutgers.edu> wrote:
>
> > On Wed, Jun 27, 2012, Brandon Sim wrote:
> >
> > >
> > > Will sander be able to snap the bond back to its equilibrium length?
> >
> > Worth a try: do minimization first, probably with SHAKE turned off.
> >
> > ...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 27 2012 - 20:30:03 PDT
