AMBER Archive (2007)

Subject: Re: Fwd: Re: AMBER: Minimization amber9 segmentation fault

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon Dec 03 2007 - 16:42:54 CST

> (actually 520 steps because I used rst). Which values of ENERGY and GMAX should
> be reached with (as in present case) protein-ligand restrained 30.0 before
> relaxing the latter? Also, should this minimization be completed with conjugate
> gradient, or is this one only to make the process faster?

There are 2 methods for minimization in AMBER; steepest descent and
conjugate gradient. It is best to use both methods in minimization because
steepest descent will quickly move the system to the local minimum
and conjugate gradient will minimize the system around the local minimum
area.

The idea of minimization is to get rid of bad contacts. If your system is
fine after minimization (whether you used conjugate gradient and/or
steepest descent), then you can do the production runs to this minimized
structure.

Best, 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  = Department of Chemistry      -                              =
  = University of Rochester      -                              =
  = Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) =
  = http://www.pas.rochester.edu/~yildirim/                     =
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