[gmx-developers] Doubts to use Gromacs as Library

Roland Schulz roland at utk.edu
Fri Sep 5 22:57:32 CEST 2014

On Fri, Sep 5, 2014 at 3:25 PM, Rodrigo Faccioli <rodrigo.faccioli at gmail.com>
> 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.


> 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]
> [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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