<p></p>
<p>----------------------------------------------------------<br>
Claudio M. Soares <br>
ITQB<br>
Instituto de Tecnologia Química e Biológica António Xavier<br>
Universidade Nova de Lisboa <br>
Av. da República, <br>
2780-157 Oeiras <br>
PORTUGAL <br>
Phone:(351)214469259/214469610/214469100 <br>
Fax :(351)214411277 <br>
<a href="mailto:email%3Aclaudio@itqb.unl.pt">email:claudio@itqb.unl.pt</a> <br>
<a href="http://www.itqb.unl.pt/~claudio">http://www.itqb.unl.pt/~claudio</a> <br>
Skype: claudio.m.soares <br>
--------------------------------------------------------</p>
<div class="gmail_quote">Em 7 de Set de 2014 22:00, "Rodrigo Faccioli" <<a href="mailto:rodrigo.faccioli@gmail.com">rodrigo.faccioli@gmail.com</a>> escreveu:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Dear prof. <span style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px">Michael Shirts, </span> <br></div><div><br></div><div>I am thankful with your email.</div><div><br></div><div>I found two issues on readmine about integrator framework and Monte Carlo framework. They are below. Could you confirm they are the issues in which I can start reading? </div><div><br></div><div>[1] <a href="http://redmine.gromacs.org/issues/1137" target="_blank">http://redmine.gromacs.org/issues/1137</a></div><div>[2] <a href="http://redmine.gromacs.org/issues/1562" target="_blank">http://redmine.gromacs.org/issues/1562</a></div><div><br></div><div>Best regards,</div><div><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="14851eac4a795aaf_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 Sat, Sep 6, 2014 at 10:16 PM, Shirts, Michael R. (mrs5pt) <span dir="ltr"><<a href="mailto:mrs5pt@eservices.virginia.edu" target="_blank">mrs5pt@eservices.virginia.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif">
<div>
<div>
<div>Hi, Rodrigo-</div>
<div><br>
</div>
<div>We've been talking and planning about better integrator frameworks and a MC framework for a while, though it's gotten hung up on lack of time for people involved. The really hard part is getting the data structures and logic right, especially in conjunction
with parallel processing -- all the algorithms themselves are pretty simple. There are a few postings on redmine, and that might be the best place to post comments and continue the discussion. I'm guessing it's not really going to be until October or November
before that effort restarts significantly.</div>
<div>
<div><br>
</div>
<div>Best,</div>
~~~~~~~~~~~~<br>
Michael Shirts<br>
Associate Professor<br>
Department of Chemical Engineering<br>
University of Virginia<br>
<a href="http://michael.shirts@virginia.edu" target="_blank">michael.shirts@virginia.edu</a><br>
<a href="tel:%28434%29-243-1821" value="+14342431821" target="_blank">(434)-243-1821</a></div>
</div>
</div>
<div><br>
</div>
<span>
<div style="font-family:Calibri;font-size:14pt;text-align:left;color:black;BORDER-BOTTOM:medium none;BORDER-LEFT:medium none;PADDING-BOTTOM:0in;PADDING-LEFT:0in;PADDING-RIGHT:0in;BORDER-TOP:#b5c4df 1pt solid;BORDER-RIGHT:medium none;PADDING-TOP:3pt">
<span style="font-weight:bold">From: </span>Rodrigo Faccioli <<a href="mailto:rodrigo.faccioli@gmail.com" target="_blank">rodrigo.faccioli@gmail.com</a>><br>
<span style="font-weight:bold">Reply-To: </span>"<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a>" <<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a>><br>
<span style="font-weight:bold">Date: </span>Saturday, September 6, 2014 at 10:41 AM<br>
<span style="font-weight:bold">To: </span>Discussion list for GROMACS development <<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [gmx-developers] Doubts to use Gromacs as Library<br>
</div><div><div>
<div><br>
</div>
<div>
<div>
<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 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 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 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)" target="_blank">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="14851eac4a795aaf_1484db3f1127bde9_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><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>> 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>
<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>
<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>><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>
<br>
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