AMBER Archive (2006)

Subject: Re: AMBER: another question: is rms 2E-2 good for nmode ntrun=1?

From: nadiav_at_soton.ac.uk
Date: Fri May 12 2006 - 11:00:21 CDT

Hi,

Just noticed this communication, and that you are intending to run NMA on a
system of 6420 atoms. I had the impression that nmode (amber 8) is limited
to 5600 atoms?? is that correct?

Nadia

Quoting "David A. Case" <case_at_scripps.edu>:

> On Fri, May 12, 2006, Pan, Yongmei wrote:
> >
> > another question for starting structure for nmode ntrun=1. After 10000
> > cycles of GB(igb=2) follwed by 10000 cycles of epsilon=4r sander
> > minimization, the rms wandered around 2E-2, and it seems that it would
> take
> > forever to reach E-3 magnitude. Is this because my molecule with 6420
> atoms
> > is too big to reach a small rms? and if the rms cannot be smaller, is
> rms
> > value 2E-2 small enough for the nmode ntrun=1 calculation?
>
> The four main options:
>
> 1. Be patient; that is, run *lots* of cycles of minimization.
> 2. Write a better minimizer.
> 3. Convince someone else to write a better minimizer.
> 4. If you have lots of memory available, NAB can minimize large
> molecules
> like this down to gradients of 10**-12 or so.
> <http://www.scripps.edc/case>.
>
> Myself, I mainly use option 1. Options 2-4 are probably better, but it's
> usually easier just to set maxcyc=100000 or so, and go have some coffee
> while
> the computer is running....
>
> ...dac
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