[gmx-developers] Doubts to use Gromacs as Library
Claudio M. Soares
claudio at itqb.unl.pt
Sun Sep 7 23:01:22 CEST 2014
----------------------------------------------------------
Claudio M. Soares
ITQB
Instituto de Tecnologia Química e Biológica António Xavier
Universidade Nova de Lisboa
Av. da República,
2780-157 Oeiras
PORTUGAL
Phone:(351)214469259/214469610/214469100
Fax :(351)214411277
email:claudio at itqb.unl.pt
http://www.itqb.unl.pt/~claudio
Skype: claudio.m.soares
--------------------------------------------------------
Em 7 de Set de 2014 22:00, "Rodrigo Faccioli" <rodrigo.faccioli at gmail.com>
escreveu:
> 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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>>>
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>>
>>
>> --
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>>
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>
>
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