AMBER Archive (2004)

Subject: Re: AMBER: Nmode convergence

From: David A. Case (case_at_scripps.edu)
Date: Tue Feb 10 2004 - 10:34:17 CST

On Tue, Feb 10, 2004, ML wrote:

> I minimize a 3000-atom protein with Newton-Raphson (after conjugate
> grad.) as I want to calculate normal modes. I use convergence criterion
> of E10-4 or 5E10-5 but for the normals modes it's much higher (E10-3 to
> 5E10-4). I understand that this has to do with re-creating the pairlist
> when restarting but how to proceed? (the same thing happened after
> conj.grad. mini)

Set your cutoff to 9999. This will make the minimization converge
more smoothly, and will remove any effect of changing cutoffs.

I generally find that conjugate gradient minimization is fine...no need
for Newton-Raphson. Just be patient (i.e. run lots of cycles of
minimization).

...good luck...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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