Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop?

From: Brandon Sim <simpavid.gmail.com>
Date: Wed, 27 Jun 2012 23:19:08 -0400

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
> >
> >
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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Wed Jun 27 2012 - 20:30:03 PDT
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