<div dir="ltr"><div>Hi Ronald, <br></div><div><br></div><div>Thanks for your feedback.</div><div><br></div><div>I will be happy and I have interested in contribute to Gromacs project.</div><div><br></div><div><span class="im" style="font-family:arial,sans-serif;font-size:13px">> 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. <br></span><span style="font-family:arial,sans-serif;font-size:13px">> We don't have a proper API for anything other than the writing analysis tools yet. We do have the other headers exported but it isn't a real >API. Do you want to keep your MC a separate project or is it an option to contribute it to Gromacs? An API for integrator extensions is still >a while in the future. We are of course always happy about contributions, but it might be quite a project to define a good API for that.</span><br></div><div><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div><div>Are you interest in develop it or similar work? Can we work together in this project and start to develop an API for integrator extensions? I am interested.<br></div><div><br></div><div><span class="im" style="font-family:arial,sans-serif;font-size:13px"><div>> 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? </div></span><div style="font-family:arial,sans-serif;font-size:13px">>Your copying the data into your structures? Without knowing the details that seems a bit inefficient (might not matter) but helps having a >better interface. Seems reasonable.</div></div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">Here I thought to add structures from Gromacs topology in my top_global_t struture. So, my project (2PG) call Gromacs function to build whole topology and I referenced it by pointer to avoid coping data. However, based on your email I believe that we can implement more efcient way. So, I guess an API or wrapper for it is a good way. </div><div><br></div><div><span class="im" style="font-family:arial,sans-serif;font-size:13px"><div>> 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.</div></span><div style="font-family:arial,sans-serif;font-size:13px">> I'm not aware of anyone having started anything.</div></div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">I would like to start it. Let me know if there is some discussion/presentation/objective about this project among developers gromacs or do I start?I have read about it what was written in [1]. </div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">[1] <a href="http://www.gromacs.org/Project_ideas#Modularize_pdb2gmx_(and_friends)">http://www.gromacs.org/Project_ideas#Modularize_pdb2gmx_(and_friends)</a></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 class="gmail_extra"><br clear="all"><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="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>
<br><div class="gmail_quote">On Fri, Sep 5, 2014 at 5:57 PM, Roland Schulz <span dir="ltr"><<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><span class=""><br><br><br>On Fri, Sep 5, 2014 at 3:25 PM, Rodrigo Faccioli <<a href="mailto:rodrigo.faccioli@gmail.com" target="_blank">rodrigo.faccioli@gmail.com</a>> wrote:<br>><br>> Hi Gromacs developers, <br>><br>><br>> Based on Gromacs project Ideas [1] and feature wishlist [2], I am interested in two projects:<br>><br>><br>> 1. Monte Carlo;<br>><br>> 2. Modularization of the program pdb2gmx.<br>><br>><br>> 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].<br>><br>><br>> 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. <br><br></span>We don't have a proper API for anything other than the writing analysis tools yet. We do have the other headers exported but it isn't a real API. Do you want to keep your MC a separate project or is it an option to contribute it to Gromacs? An API for integrator extensions is still a while in the future. We are of course always happy about contributions, but it might be quite a project to define a good API for that.<div><br></div><div><span class="">> More specific, I would like to get help in two parts:<br>><br>> How can I remove Gromacs system calls using Gromacs API?<br><br></span>Not sure what you mean with that.</div><span class=""><div><br>> 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? </div><div><br></div></span><div>Your copying the data into your structures? Without knowing the details that seems a bit inefficient (might not matter) but helps having a better interface. Seems reasonable.</div><span class=""><div><br>><br>> 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. <br>><br>><br>> 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.</div><div><br></div></span><div>I'm not aware of anyone having started anything.</div><div><br></div><div>Roland</div><div><br></div><div><span class="">><br>><br>> I've seen that Mone Carlo there is 1137 issue [7]. Nonetheless, I haven't found for Modularization of the program pdb2gmx.<br>><br>><br>><br>> [1] <a href="http://www.gromacs.org/Project_ideas" target="_blank">http://www.gromacs.org/Project_ideas</a><br>><br>> [2] <a href="http://www.gromacs.org/Developer_Zone/Roadmap/Feature_wishlist" target="_blank">http://www.gromacs.org/Developer_Zone/Roadmap/Feature_wishlist</a><br>> [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><br>> [4] <a href="http://lcrserver.icmc.usp.br/projects/2pg_cartesian" target="_blank">http://lcrserver.icmc.usp.br/projects/2pg_cartesian</a><br>> [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><br>> [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><br>> [7] <a href="http://redmine.gromacs.org/issues/1137" target="_blank">http://redmine.gromacs.org/issues/1137</a><br>><br>><br>> Best regards,<br>><br>> --<br>> Rodrigo Antonio Faccioli, Ph.D<br>> Development Software for Structural Biology<br>> Barao de Maua University<br>> University of Sao Paulo<br>> Lindedin - <a href="http://br.linkedin.com/pub/rodrigo-antonio-faccioli/7/589/a5/" 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><br><br><br><br></span>--<br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a><br><a href="tel:865-241-1537" value="+18652411537" target="_blank">865-241-1537</a>, ORNL PO BOX 2008 MS6309<br></div></div>
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