AMBER Archive (2008)

Subject: Re: AMBER: Minimization methods

From: teresa.ierano_at_unina.it
Date: Mon Aug 11 2008 - 11:39:30 CDT

Thank you Mr Dodson...besides Ross Walker's answer, you further
clarify my doubt!

Quoting "M. L. Dodson" <activesitedynamics_at_comcast.net>:

> 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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