Sorry my delay.<br><br>Now it's working fine. thanks all people who helped.<br><br>Thanks in advance,<br><br clear="all">--<br>Rodrigo Antonio Faccioli<br>Ph.D Student in Electrical Engineering<br>University of Sao Paulo - USP<br>
Engineering School of Sao Carlos - EESC<br>Department of Electrical Engineering - SEL<br>Intelligent System in Structure Bioinformatics<br><a href="http://laips.sel.eesc.usp.br">http://laips.sel.eesc.usp.br</a><br>Phone: 55 (16) 3373-9366 Ext 229<br>
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<br><br><div class="gmail_quote">On Wed, Jun 2, 2010 at 5:14 AM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br><br>----- Original Message -----<br>From: Rodrigo Faccioli <<a href="mailto:rodrigo_faccioli@uol.com.br" target="_blank">rodrigo_faccioli@uol.com.br</a>><br>Date: Wednesday, June 2, 2010 15:53<br>
Subject: [gmx-developers] New integrator applying Multi-Objective Evolutionary Algorithm<br>To: Discussion list for GROMACS development <<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a>><br>
<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Hi,<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>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. <br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>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.<br>
<br></div>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.<div class="im">
<br><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Basically, those are my changes in the source code.<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>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<br>
<br></div>Yep, that's what git grompp does when you break it.<br><br>Mark<div class="im"><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;"> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>[1] <a href="http://gitorious.org/protpred-peo/gromacs/" target="_blank">http://gitorious.org/protpred-peo/gromacs/</a><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>[2] <a href="http://www.gromacs.org/Developer_Zone/Programming_Guide/Programmers%27s_Guide" target="_blank">http://www.gromacs.org/Developer_Zone/Programming_Guide/Programmers%27s_Guide</a><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> [3] <a href="http://pastebin.com/fSb7HFVP" target="_blank">http://pastebin.com/fSb7HFVP</a><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Thanks in advance,<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br clear="all">
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>--<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Rodrigo Antonio Faccioli<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Ph.D Student in Electrical Engineering<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>University of Sao Paulo - USP<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Engineering School of Sao Carlos - EESC<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Department of Electrical Engineering - SEL<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Intelligent System in Structure Bioinformatics<br><a href="http://laips.sel.eesc.usp.br" target="_blank"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>http://laips.sel.eesc.usp.br</a><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Phone: 55 (16) 3373-9366 Ext 229<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Curriculum Lattes - <a href="http://lattes.cnpq.br/1025157978990218" target="_blank">http://lattes.cnpq.br/1025157978990218</a><br>
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