[gmx-developers] Doubts to use Gromacs as Library

Sat Sep 6 16:41:28 CEST 2014

Hi Ronald,

Thanks for your feedback.

I will be happy and I have interested in contribute to Gromacs project.

> 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.
> 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.

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.

> 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?
>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.

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.

> 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.
> I'm not aware of anyone having started anything.

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].

[1] http://www.gromacs.org/Project_ideas#Modularize_pdb2gmx_(and_friends)

Best regards,

--
Rodrigo Antonio Faccioli, Ph.D
Development Software for Structural Biology
Barao de Maua University
University of Sao Paulo
Lindedin - br.linkedin.com/pub/rodrigo-antonio-faccioli/7/589/a5/
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218

On Fri, Sep 5, 2014 at 5:57 PM, Roland Schulz <roland at utk.edu> wrote:

>
>
>
> On Fri, Sep 5, 2014 at 3:25 PM, Rodrigo Faccioli <
> rodrigo.faccioli at gmail.com> wrote:
> >
> > Hi Gromacs developers,
> >
> >
> > Based on Gromacs project Ideas [1] and feature wishlist [2], I am
> interested in two projects:
> >
> >
> > 1. Monte Carlo;
> >
> > 2. Modularization of the program pdb2gmx.
> >
> >
> > 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].
> >
> >
> > 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.
>
> 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.
>
> > More specific, I would like to get help in two parts:
> >
> > How can I remove Gromacs system calls using Gromacs API?
>
> Not sure what you mean with that.
>
> > 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?
>
> 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.
>
> >
> > 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.
> >
> >
> > 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.
>
> I'm not aware of anyone having started anything.
>
> Roland
>
> >
> >
> > I've seen that Mone Carlo there is 1137 issue [7]. Nonetheless, I
> haven't found for Modularization of the program pdb2gmx.
> >
> >
> >
> > [1] http://www.gromacs.org/Project_ideas
> >
> > [2] http://www.gromacs.org/Developer_Zone/Roadmap/Feature_wishlist
> > [3]
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2013-September/007089.html
> > [4] http://lcrserver.icmc.usp.br/projects/2pg_cartesian
> > [5] https://www.dropbox.com/s/z3z86h6jma1okid/all_typedef.png?dl=0
> > [6] https://www.dropbox.com/s/red11o3fr6h4lyo/nsga2_typedef.png?dl=0
> > [7] http://redmine.gromacs.org/issues/1137
> >
> >
> > Best regards,
> >
> > --
> > Rodrigo Antonio Faccioli, Ph.D
> > Development Software for Structural Biology
> > Barao de Maua University
> > University of Sao Paulo
> > Lindedin - br.linkedin.com/pub/rodrigo-antonio-faccioli/7/589/a5/
> > Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
>
>
>
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309
>
> --
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