[gmx-developers] Doubts to use Gromacs as Library

Rodrigo Faccioli rodrigo.faccioli at gmail.com
Fri Sep 5 21:25:27 CEST 2014

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.

More specific, I would like to get help in two parts:

   1. How can I remove Gromacs system calls using Gromacs API?
   2. 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?

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'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
[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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20140905/84ca790a/attachment.html>

More information about the gromacs.org_gmx-developers mailing list