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

[Jeff Hammond]

Generically, the best way to contribute to a Git-hosted project is to:
1) git clone <the repo>
2) make some changes
3) run all the regression tests to make sure you haven't broken something
4) git commit -a # write a helpful commit message - see stackoverflow, etc.
for style guides
5) git format-patch origin
6) send patch files to the appropriate person/list or attach to ticket if
it's fixing something

So far, this has worked great for my trivial contributions to Gromacs.

Best,

Jeff


On Fri, Aug 23, 2013 at 9:41 AM, Rodrigo Faccioli <
rodrigo_faccioli at uol.com.br> wrote:

> 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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>> > gmx-developers at gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-developers
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>
>
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-- 
Jeff Hammond
jeff.science at gmail.com
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