AMBER Archive (2002)

Subject: Re: minimization in amber7 for nonperiodic systems

From: David A. Case (case_at_scripps.edu)
Date: Wed Aug 14 2002 - 10:28:21 CDT

On Wed, Aug 14, 2002, Giulio Rastelli wrote:

> Also by using a short cutoff and by setting nbflag=0 and skinnb=0 (2),
> which restores the use of the non-bonded
> list update, I didn't have any failure in minimization;
> I also tested the difference between (1) and (2) with molecular dynamics
> at 300K:

Note that I am *not* sure it is a good idea to use nbflag=0 for MD; there you
can (sort of) live with the "noise" induced by essentially updating the list
every step (which is logically what the default behavior gives). This is
somewhat in line with your observation that using more frequent updates in MD
seems to help. I am only recommending nbflag=0, skinnb=0. for minimization,
not for dynamics.

...thanks for your input....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
==================================================================