[gmx-developers] New integrator applying Multi-Objective Evolutionary Algorithm

[Rodrigo Faccioli]

Sorry my delay.

Now it's working fine.  thanks all people who helped.

Thanks in advance,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5


On Wed, Jun 2, 2010 at 5:14 AM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

>
>
> ----- Original Message -----
> From: Rodrigo Faccioli <rodrigo_faccioli at uol.com.br>
> Date: Wednesday, June 2, 2010 15:53
> Subject: [gmx-developers] New integrator applying Multi-Objective
> Evolutionary Algorithm
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
>
> > Hi,
> >
> > We are trying to develop a new integrator option in GROMACS based on
> NSGA-II algorithm. This algorithm is a MOEA (Multi-Objective Evolutionary
> Algorithm). Our repository can be accessed in [1]. If you want more
> information about it, I can send our documentation.
> >
> > I tried to study the md integrator. I developed do_ea function in md.c.
> However, that function has a message only. We want to execute do_ea function
> instead of do_md function.  In this way I found in [2] some informations
> about how mdrun works which I'm studying. Already on grompp I couldn't find
> almost anything, except how add new parameter. So, I changed name.c file
> only adding "ea" option in ei_names variable.  Furthermore, I added eiEA
> enum before eiNR.
>
> Your git repo hasn't updated eiNR, so the compiler should complain about
> the number of array initializers being wrong. Find the header file that
> defines the enum with eiNR. This must match the array of names, since that's
> how grompp matches an input string to an int that you can later test for
> when choosing the integrator.
>
>
> > Basically, those are my changes in the source code.
> >
> > I show the error message together my mdp file in [3] when I ran:
> /home/faccioli/workspace/gromacs/src/kernel/grompp -f minimization.mdp -c
> teste.gro -p teste.top -o ea_0.tpr
>
> Yep, that's what git grompp does when you break it.
>
> Mark
>
>
> > [1] http://gitorious.org/protpred-peo/gromacs/
> > [2]
> http://www.gromacs.org/Developer_Zone/Programming_Guide/Programmers%27s_Guide
> > [3] http://pastebin.com/fSb7HFVP
> >
> > Thanks in advance,
> >
> > --
> > Rodrigo Antonio Faccioli
> > Ph.D Student in Electrical Engineering
> > University of Sao Paulo - USP
> > Engineering School of Sao Carlos - EESC
> > Department of Electrical Engineering - SEL
> > Intelligent System in Structure Bioinformatics
> > http://laips.sel.eesc.usp.br <http://laips.sel.eesc.usp.br>
> > Phone: 55 (16) 3373-9366 Ext 229
> > Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
> > Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
> > --
> > gmx-developers mailing list
> > gmx-developers at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-developers
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