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

[Mark Abraham]

----- 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
> 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
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-developers-request at gromacs.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20100602/b383f0c8/attachment.html>