AMBER Archive (2008)

Subject: Re: AMBER: Minimization methods

From: M. L. Dodson (activesitedynamics_at_comcast.net)
Date: Mon Aug 11 2008 - 10:34:05 CDT

E.M. wrote:
> uh?. This question does not make any sense!!!
>

I fail to see how it does not make sense. As Ross has indicated, it
was arbitrary in this case, but that does not make it a nonsense
question.

If a serious minimization procedure involves two different
optimization algorithms, one that works better far away from the
minimum and one that works better close to the minimum, the choice of
a good "switchover function" can be decidedly nontrivial (as a review
of the function optimization literature will reveal). That it was
arbitrary in this specific case does not change the validity of asking
how the tutorial designer (Ross) came up with the "switchover
function".

Bud Dodson

>
> teresa.ierano_at_unina.it wrote:
>> Hi all,
>> I would like to know why in solvent minimization reported in Amber
>> tutorials the same number of steps are used for the steepest descent
>> and conjugate gradient algorithms.
>> Thank you for your reply,
>> Best regards. 

-- 
M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
Personal Email:	mldodson-at-comcast-dot-net
Phone:	eight_three_two-56_three-386_one
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