[gmx-developers] How can use GROMACS into applications - Better way

[Rodrigo Faccioli]

Hi Mark,

Thanks your answer.

We are glad to contribute with Gromacs. We would like to try to do it.

What do you suggest for us about rules to contribute with Gromacs?

I have read in Developers zone at Gromacs site about Gerrit and Git. It is
the best way?

Best regards,



--
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


On Wed, Aug 21, 2013 at 5:04 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> Hi,
>
> Thanks for your interest. Unfortunately, there's never really been a
> callable API for GROMACS. The core team has always prioritized higher
> performance and new features over facilitating third-party code re-use
> - manpower resources are limiting. There's hope we can improve this in
> the future during the C++ transition... e.g.
> http://redmine.gromacs.org/issues/988,
> http://redmine.gromacs.org/issues/1140.
>
> In particular, http://redmine.gromacs.org/issues/1170 suggests being
> able to remove the "middle man" of writing a .tpr file. It sounds like
> your use case would be streamlined a lot if it were possible to pass
> "grompp" whatever inputs are easily constructed by your code, and the
> output of "grompp" are data structures ready for "mdrun." mdrun in 5.0
> might support this already, which would be useful for you, but not yet
> ideal.
>
> If you'd like to contribute, that would be fantastic. A sketch in
> http://redmine.gromacs.org/issues/1140 of a series of hypothetical
> function calls you'd like to make in order to execute your workflow
> would be a great start. Having an external need described should help
> us prioritise what we can do.
>
> Cheers,
>
> Mark
>
> On Tue, Aug 20, 2013 at 9:04 PM, Rodrigo Faccioli
> <rodrigo_faccioli at uol.com.br> wrote:
> > Hi Gromacs Developers,
> >
> > We have worked in a framework that uses Evolutionary Algorithms (EA) with
> > GROMACS. This frameword is called ProtPred-Gromacs (2PG) [1].
> >
> > In general lines, GROMACS is used to compute the objetives of individual
> > (protein conformation). Potential, Van der Waals, Electrostatic, GBSA
> > Solvatation, Hydrophobic, Hydrophilic, Gyrate and Hydrogen Bonds are
> > examples of objetives.
> >
> > Nowadays, those objetives are computed by scripts that calls the
> respective
> > GROMACS program for each objective.  I call a system command and load the
> > GROMACS program output into my structure.
> >
> > I would like to know a way that is possible to remove those scripts. I
> have
> > read about C++ transition at GROMACS page [2]. However, I could not
> > understand how I can use it in my project.
> >
> > Therefore, I would like to ask some examples, tips or any other comments
> > about a way to remove the scripts and I get the objetives with more
> > performance.
> >
> > [1] http://lcrserver.icmc.usp.br/projects/2pg
> > [2]
> http://www.gromacs.org/index.php?title=Developer_Zone/C%2b%2b_Transition
> >
> > Best regards,
> >
> > --
> > Rodrigo Antonio Faccioli, Ph.D
> > Intelligent System in Structural Bioinformatics
> > University of Sao Paulo - USP
> > Barao de Maua University
> > Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
> > Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
> > Personal Blogg - http://rodrigofaccioli.blogspot.com/
> >
> >
> > --
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