Re: [AMBER] Minimization in sander

From: David A Case <case.biomaps.rutgers.edu>
Date: Wed, 2 Nov 2011 09:58:38 -0400

On Wed, Nov 02, 2011, Anglea A. wrote:

> The NSTEP is the final result.
> The input of my job is:
>  &cntrl
>
>  imin   = 1,
>  maxcyc = 100000,
>  drms   = 1.0E-5,
>  ntb    = 0,
>  ntmin = 3,
>  cut    = 15.0,
>  ntb=0,
>  igb=0,
> /
>  &lmod
>  xmin_method = "LBFGS"

I'd recommend setting maxcyc to 500 or so, and ntpr to 10 (or even 1), and
following the course of the minimization. You have a vacuum system, so
using cut of 9999. (essentially infinite) might also be necessary.

The xmin defaults are almost always fine...I wouldn't worry about them.
The fact that your minimization ended after only 27 steps suggests some
problem (my guess is that it is the cutoff, but look in the output for clues.)

...dac


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Received on Wed Nov 02 2011 - 07:00:03 PDT
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