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

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 27 Jun 2012 23:39:43 -0400

On Wed, Jun 27, 2012 at 11:19 PM, Brandon Sim <simpavid.gmail.com> wrote:

> Dear Jason,
>
> Is ncyc > 100 better? I'm currently running ncyc=500, maxcyc=1000
>

It all depends on what you're trying to do. If you're trying to minimize
to start dynamics, it likely doesn't matter. ncyc = 100, maxcyc = 1000
will most likely converge to a lower-energy structure than
ncyc=500/maxcyc=1000, but for dynamics I'm pretty sure either will do. The
default value is 10, which can be too small for some highly strained
structures, but my thought is that if 100 can't do it, you're in for an
interesting time...

All the best,
Jason

-- 
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 - 21:00:02 PDT
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