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

Mark Abraham mark.j.abraham at gmail.com
Wed Aug 21 10:04:00 CEST 2013


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.

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

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.



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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