Subject: Re: CCL:Genetic Algorithm routine ?

From: "tek kno3" <[email-masked]>
Date: Thu, 21 Jun 2001 00:55:05 -0300

>It is about Genetic Algorithm (GA) implemented in AutoDock. There
>are "population", "max evaluations", "elitism" ,etc.
>
>Does "max evaluations" determinates the max energy evaluations needed
>to produce a population? Could anyone explain briefly and the essence
>of routine GA?

Hi,

you should take a look at the code/manual but usualy "max evaluations" are 
the maximum number o generations, i.e., GA optimization steps (each step 
should consist of (number of individuals in "population") energy 
evaluations).

GA work throught selection of the fittest. In general, an initial 
population, i.e. a group of individuals (which genes correspond to the 
paramethers one wishes to optimize) is evaluated accordingly to your error 
function (e.g. energy difference, etc), then the fittest (e.g. lowest energy 
difference, etc) individuals are reproduced to the next generation 
accordingly to some genetics rules (breeding, mutation, etc). This evolution 
process continues till convergence or "max evaluations/generations".

For a more complete review check:

Rev.Comp.Chem. 10 (1997) - Richard Judson, Genetic Algorithms and Their Use 
in Chemistry, pp. 1-73.

or just do a web search...

hope it helps, cheers,

Guilherme Menegon
IQUSP - Brazil

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