<div dir="ltr"><div style><p style="font-family:arial,sans-serif;font-size:13px;margin:0px">Hi Gromacs developers, </p><p style="font-family:arial,sans-serif;font-size:13px;margin:0px"><br></p><p style="font-family:arial,sans-serif;font-size:13px;margin:0px">Based on Gromacs project Ideas [1] and feature wishlist [2], I am interested in two projects:</p><p style="font-family:arial,sans-serif;font-size:13px;margin:0px"><br></p><p style="font-family:arial,sans-serif;font-size:13px;margin:0px">1. Monte Carlo;<br></p><p style="font-family:arial,sans-serif;font-size:13px;margin:0px">2. Modularization of the program pdb2gmx.<br></p><p style="font-family:arial,sans-serif;font-size:13px;margin:0px"><br></p><p style="font-family:arial,sans-serif;font-size:13px;margin:0px">In Monte Carlo, I would like to work with Gromacs 5 API integrated with my Monte Carlo implementation. Nowadays, my implementation uses Gromacs 4.6. I have already commented here about the first version of my project [3]. However, It was updated totally. Its new version can be found in [4].</p><p style="font-family:arial,sans-serif;font-size:13px;margin:0px"><br></p><p style="font-family:arial,sans-serif;font-size:13px;margin:0px">I have read about Gromacs 5 as library But, I am not sure what is the best way to implement it in my project. In [5] is an image of my data structure. In solution_t, representation field stores a protein conformation (protein_t) that is computed by Gromacs (here Gromacs is called by simple system commands) the potencial energy of this conformation. This energy value is stored at obj_values field. </p><p style="font-family:arial,sans-serif;font-size:13px;margin:0px"><br></p><p style="font-family:arial,sans-serif;font-size:13px;margin:0px">More specific, I would like to get help in two parts:</p><p style="font-family:arial,sans-serif;font-size:13px;margin:0px"></p><ol style="font-family:arial,sans-serif;font-size:13px"><li>How can I remove Gromacs system calls using Gromacs API?<br></li><li>Based on Gromacs API, is it a good practice modify my pdb_atom_t and top_global_t data structures for their respective Gromacs structures? </li></ol><p style="font-family:arial,sans-serif;font-size:13px"></p><p style="margin:0px"><font face="arial, sans-serif">It is important to emphasize that all implemented algorithms in my project, they use solution_t data structure to represent a solution that is a protein conformation or polymer (next release). For example, in [6] is the data structure of NSGA-II algorithm (it is multi-objective evolutionary algorithm). In this case ea_nsga2_t means an individual. Therefore, in obj_values field is stored more than one value of protein conformation such as Potential, Gyrate, number of Hydrogen Bond and others. All values are calculated by Gromacs. </font><br></p><p style="font-family:arial,sans-serif;font-size:13px;margin:0px"><br></p><p style="font-family:arial,sans-serif;font-size:13px;margin:0px">My second interest is Modularization of the program pdb2gmx. I would like to know about developers that have been working with it since I would like to participate/attend to this project idea.</p><p style="font-family:arial,sans-serif;font-size:13px;margin:0px"><br></p><p style="font-family:arial,sans-serif;font-size:13px;margin:0px">I've seen that Mone Carlo there is 1137 issue [7]. Nonetheless, I haven't found for Modularization of the program pdb2gmx.</p><p style="font-family:arial,sans-serif;font-size:13px;margin:0px"><br></p><p style="font-family:arial,sans-serif;font-size:13px;margin:0px"><br></p><p style="font-family:arial,sans-serif;font-size:13px;margin:0px">[1] <a href="http://www.gromacs.org/Project_ideas" target="_blank">http://www.gromacs.org/Project_ideas</a></p></div><div style="font-family:arial,sans-serif;font-size:13px">[2] <a href="http://www.gromacs.org/Developer_Zone/Roadmap/Feature_wishlist" target="_blank">http://www.gromacs.org/Developer_Zone/Roadmap/Feature_wishlist</a></div><div style="font-family:arial,sans-serif;font-size:13px">[3] <a href="https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2013-September/007089.html" target="_blank">https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2013-September/007089.html</a></div><div style="font-family:arial,sans-serif;font-size:13px">[4] <a href="http://lcrserver.icmc.usp.br/projects/2pg_cartesian" target="_blank">http://lcrserver.icmc.usp.br/projects/2pg_cartesian</a></div><div style="font-family:arial,sans-serif;font-size:13px">[5] <a href="https://www.dropbox.com/s/z3z86h6jma1okid/all_typedef.png?dl=0" target="_blank">https://www.dropbox.com/s/z3z86h6jma1okid/all_typedef.png?dl=0</a></div><div style="font-family:arial,sans-serif;font-size:13px">[6] <a href="https://www.dropbox.com/s/red11o3fr6h4lyo/nsga2_typedef.png?dl=0" target="_blank">https://www.dropbox.com/s/red11o3fr6h4lyo/nsga2_typedef.png?dl=0</a></div><div style="font-family:arial,sans-serif;font-size:13px">[7] <a href="http://redmine.gromacs.org/issues/1137">http://redmine.gromacs.org/issues/1137</a></div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">Best regards,</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div><div dir="ltr">--<br>Rodrigo Antonio Faccioli, Ph.D<br>Development Software for Structural <span style="color:rgb(51,51,51);font-family:Helvetica,FreeSans,'Liberation Sans',Helmet,Arial,sans-serif;line-height:17px">Biology</span><br>Barao de Maua University<div>University of Sao Paulo<br><div>Lindedin - <a href="http://br.linkedin.com/pub/rodrigo-antonio-faccioli/7/589/a5/" title="View public profile" name="1484321b0003e93d_SafeHtmlFilter_webProfileURL" target="_blank">br.linkedin.com/pub/rodrigo-antonio-faccioli/7/589/a5/</a><br>Curriculum Lattes - <a href="http://lattes.cnpq.br/1025157978990218" target="_blank">http://lattes.cnpq.br/1025157978990218</a><br></div></div></div></div>
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