[gmx-developers] Doubts to use Gromacs as Library
Rodrigo Faccioli
rodrigo.faccioli at gmail.com
Sun Sep 7 22:59:39 CEST 2014
Dear prof. Michael Shirts,
I am thankful with your email.
I found two issues on readmine about integrator framework and Monte Carlo
framework. They are below. Could you confirm they are the issues in which I
can start reading?
[1] http://redmine.gromacs.org/issues/1137
[2] http://redmine.gromacs.org/issues/1562
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 Sat, Sep 6, 2014 at 10:16 PM, Shirts, Michael R. (mrs5pt) <
mrs5pt at eservices.virginia.edu> wrote:
> Hi, Rodrigo-
>
> We've been talking and planning about better integrator frameworks and a
> MC framework for a while, though it's gotten hung up on lack of time for
> people involved. The really hard part is getting the data structures and
> logic right, especially in conjunction with parallel processing -- all the
> algorithms themselves are pretty simple. There are a few postings on
> redmine, and that might be the best place to post comments and continue the
> discussion. I'm guessing it's not really going to be until October or
> November before that effort restarts significantly.
>
> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Associate Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821
>
> From: Rodrigo Faccioli <rodrigo.faccioli at gmail.com>
> Reply-To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
> Date: Saturday, September 6, 2014 at 10:41 AM
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] Doubts to use Gromacs as Library
>
> 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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