Doubts to use Gromacs as Library

Discussion:

Rodrigo Faccioli

2014-09-05 19:25:24 UTC

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
[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] Loading Image...

[6] Loading Image...

[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

Roland Schulz

2014-09-05 20:57:07 UTC

Permalink

Post by Rodrigo Faccioli
Hi Gromacs developers,
Based on Gromacs project Ideas [1] and feature wishlist [2], I am
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].

Post by Rodrigo Faccioli
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.

Post by Rodrigo Faccioli
How can I remove Gromacs system calls using Gromacs API?

Not sure what you mean with that.

Post by Rodrigo Faccioli
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.

Post by Rodrigo Faccioli
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.

Post by Rodrigo Faccioli
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

Post by Rodrigo Faccioli
I've seen that Mone Carlo there is 1137 issue [7]. Nonetheless, I haven't

found for Modularization of the program pdb2gmx.

Post by Rodrigo Faccioli
[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

Post by Rodrigo Faccioli
[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

Rodrigo Faccioli

2014-09-06 14:41:25 UTC

Permalink

Hi Ronald,

Thanks for your feedback.

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

Post by Rodrigo Faccioli
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

Post by Rodrigo Faccioli
structure. In solution_t, representation field stores a protein

conformation (protein_t) that is computed by Gromacs (here Gromacs is

Post by Rodrigo Faccioli
called by simple system commands) the potencial energy of this

conformation. This energy value is stored at obj_values field.

Post by Rodrigo Faccioli
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.

Post by Rodrigo Faccioli
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?

Post by Rodrigo Faccioli
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.

Post by Rodrigo Faccioli
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.

Post by Rodrigo Faccioli
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

Post by Rodrigo Faccioli
On Fri, Sep 5, 2014 at 3:25 PM, Rodrigo Faccioli <

Post by Rodrigo Faccioli
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.

Post by Rodrigo Faccioli
How can I remove Gromacs system calls using Gromacs API?

Not sure what you mean with that.

Post by Rodrigo Faccioli
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.

Post by Rodrigo Faccioli
It is important to emphasize that all implemented algorithms in my

Post by Rodrigo Faccioli
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

Post by Rodrigo Faccioli
I've seen that Mone Carlo there is 1137 issue [7]. Nonetheless, I

haven't found for Modularization of the program pdb2gmx.

Post by Rodrigo Faccioli
[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

--
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
--
Gromacs Developers mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
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Shirts, Michael R. (mrs5pt)

2014-09-07 01:16:00 UTC

Permalink

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
***@virginia.edu
(434)-243-1821

From: Rodrigo Faccioli <***@gmail.com<mailto:***@gmail.com>>
Reply-To: "gmx-***@gromacs.org<mailto:gmx-***@gromacs.org>" <gmx-***@gromacs.org<mailto:gmx-***@gromacs.org>>
Date: Saturday, September 6, 2014 at 10:41 AM
To: Discussion list for GROMACS development <gmx-***@gromacs.org<mailto:gmx-***@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/<http://br.linkedin.com/pub/rodrigo-antonio-faccioli/7/589/a5/>
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218

Hi Gromacs developers,
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.

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/<http://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<http://cmb.ornl.gov>
865-241-1537<tel:865-241-1537>, ORNL PO BOX 2008 MS6309

--
Gromacs Developers mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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Rodrigo Faccioli

2014-09-07 20:59:36 UTC

Permalink

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) <

Post by Shirts, Michael R. (mrs5pt)
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
(434)-243-1821
Date: Saturday, September 6, 2014 at 10:41 AM
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.

Post by Rodrigo Faccioli
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

Post by Rodrigo Faccioli
structure. In solution_t, representation field stores a protein

conformation (protein_t) that is computed by Gromacs (here Gromacs is

Post by Rodrigo Faccioli
called by simple system commands) the potencial energy of this

conformation. This energy value is stored at obj_values field.

Post by Rodrigo Faccioli
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.

Post by Rodrigo Faccioli
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?

Post by Rodrigo Faccioli
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.

Post by Rodrigo Faccioli
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.

Post by Rodrigo Faccioli
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

Post by Rodrigo Faccioli
On Fri, Sep 5, 2014 at 3:25 PM, Rodrigo Faccioli <

Post by Rodrigo Faccioli
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.

Post by Rodrigo Faccioli
How can I remove Gromacs system calls using Gromacs API?

Not sure what you mean with that.

Post by Rodrigo Faccioli
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.

Post by Rodrigo Faccioli
It is important to emphasize that all implemented algorithms in my

Post by Rodrigo Faccioli
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

Post by Rodrigo Faccioli
I've seen that Mone Carlo there is 1137 issue [7]. Nonetheless, I

haven't found for Modularization of the program pdb2gmx.

Post by Rodrigo Faccioli
[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

--
Gromacs Developers mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
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Claudio M. Soares

2014-09-07 21:01:18 UTC

Permalink

----------------------------------------------------------
Claudio M. Soares
ITQB
Instituto de Tecnologia QuÃmica e BiolÃ³gica AntÃ³nio Xavier
Universidade Nova de Lisboa
Av. da RepÃºblica,
2780-157 Oeiras
PORTUGAL
Phone:(351)214469259/214469610/214469100
Fax :(351)214411277
email:***@itqb.unl.pt
http://www.itqb.unl.pt/~claudio
Skype: claudio.m.soares
--------------------------------------------------------

Post by Rodrigo Faccioli
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) <

Post by Shirts, Michael R. (mrs5pt)
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
(434)-243-1821
Date: Saturday, September 6, 2014 at 10:41 AM
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.