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

[Rodrigo Faccioli]

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.

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
**
[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
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
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