[gmx-users] Monte Carlo with Gromacs and implicit solvent

Gianluca Interlandi gianluca at u.washington.edu
Tue Jan 24 20:33:11 CET 2012


Thanks Renè and Mark,

I will look at both options, GromPy and mdrun -rerun.

Gianluca

On Tue, 24 Jan 2012, René Pool wrote:

> By the way, the tutorial can be found on the wiki page at
> https://github.com/GromPy/GromPy/wiki/Tutorial:-Using-GromPy-in-GCMC-mode.
> 
> =====================================================
> René Pool
> 
> Division of Molecular and Computational Toxicology
> Department of Chemistry and Pharmaceutical Sciences
> Vrije Universiteit Amsterdam
> De Boelelaan 1083
> 1081HV AMSTERDAM, the Netherlands
> -----
> IBIVU/Bioinformatics
> Department of Computer Science
> Vrije Universiteit Amsterdam
> De Boelelaan 1081a
> 1081HV AMSTERDAM, the Netherlands
> 
> Room P 2.75
> E: r.pool at vu.nl
> T: +31 20 598 76 12
> F: +31 20 598 76 10
> =====================================================
> 
> On 01/24/2012 09:30 AM, Pool, R. wrote:
>       Hi Gianluca,
>
>       You might want to take a look at GromPy
>       (https://github.com/GromPy/GromPy).
>       This is a python interface to the GROMACS library. Amongst other
>       applications, there is an option to perform grand-canonical Monte Carlo
>       using GromPy. The necessary energy evaluations are performed using direct
>       library calls to GROMACS. In this way it is possible to get around the
>       possibly prohibitive file I/O in shell implementations that use the
>       GROMACS executables. A paper on GromPy and GromPy/GCMC has recently been
>       accepted in JCC, so more details will follow. In the meantime you can
>       have a look at the code and the tutorial on the above website.
>
>       Good luck!
>
>       Cheers,
>       Rene
>       =====================================================
>       René Pool
>
>       Division of Molecular and Computational Toxicology
>       Department of Chemistry and Pharmaceutical Sciences
>       Vrije Universiteit Amsterdam
>       De Boelelaan 1083
>       1081HV AMSTERDAM, the Netherlands
>       -----
>       IBIVU/Bioinformatics
>       Department of Computer Science
>       Vrije Universiteit Amsterdam
>       De Boelelaan 1081a
>       1081HV AMSTERDAM, the Netherlands
>
>       Room P 2.75
>       E: r.pool at vu.nl
>       T: +31 20 598 76 12
>       F: +31 20 598 76 10
>       =====================================================
> 
> _____________________________________________________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf
> of Rodrigo Faccioli [rodrigo_faccioli at uol.com.br]
> Sent: 24 January 2012 05:29
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent
> 
> Hi Gianluca,
> 
> I forgot to say that the step of compute the energies is considered from
> pdb2gmx until g_energy.
> 
> Sorry about my oblivion.
> 
> Best regards,
> 
> --
> Rodrigo Antonio Faccioli
> Ph.D Student in Electrical Engineering
> University of Sao Paulo - USP
> Engineering School of Sao Carlos - EESC
> Department of Electrical Engineering - SEL
> Intelligent System in Structure Bioinformatics
> http://laips.sel.eesc.usp.br
> Phone: 55 (16) 3373-9366 Ext 229
> Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
> Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
> 
> 
> On Tue, Jan 24, 2012 at 1:07 AM, Rodrigo Faccioli <rodrigo_faccioli at uol.com.br>
> wrote:
>       Hi Gianluca,
>
>       Thanks your question.
>
>       All steps to obtain a generation with 200 individuals, on average,
>       is 6 minutes for 1VII, example. In each generation I must 
>       converted my proteins Dihedral to Cartesian representation, compute
>       the energies, choose the individuals which will go to reproduction,
>       save previous population. This test was using one core of a
>       conventional Desktop computer.
>
>       The proteins, that I have tested my algorithm, vary from 20 to 56
>       amino acids.
>
>       Best regards,
>
>       --
>       Rodrigo Antonio Faccioli
>       Ph.D Student in Electrical Engineering
>       University of Sao Paulo - USP
>       Engineering School of Sao Carlos - EESC
>       Department of Electrical Engineering - SEL
>       Intelligent System in Structure Bioinformatics
>       http://laips.sel.eesc.usp.br
>       Phone: 55 (16) 3373-9366 Ext 229
>       Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
>       Public Profile -
>       http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
> 
> 
> On Tue, Jan 24, 2012 at 12:36 AM, Gianluca Interlandi
> <gianluca at u.washington.edu> wrote:
>       Thanks Enrico!
>
>       Just wondering. How fast is it? Calling gromacs must have a
>       lot of overhead. Also, do you call mdrun or does g_energy
>       evaluate the energy?
>
>       Gianluca
>
>       On Tue, 24 Jan 2012, Rodrigo Faccioli wrote:
>
>             Hi,
>
>             Although I don't work with MC simulation, I have
>             used Gromacs to obtain energies and others
>             protein features in my Evolutionary Algorithms
>             (EA).
>
>             In general lines, I created a script that calls
>             Gromacs programs and the output of these
>             programs, such as g_energy (I read its xvg file),
>             I stored it at a specific file which is
>             read by my algorithm and its values are put into
>             my data structure. I call Gromacs either
>             implicit or explicit solvent. 
>
>             My project is working with EA until now. However,
>             the integration with GROMACS is able to
>             work with other kind of algorithms such as MC.
>             Actually, we have idea to work with MC. But,
>             I don't know when it will be possible. If you
>             want, we can talk about join these work.
>
>             Best regards,
>
>             --
>             Rodrigo Antonio Faccioli
>             Ph.D Student in Electrical Engineering
>             University of Sao Paulo - USP
>             Engineering School of Sao Carlos - EESC
>             Department of Electrical Engineering - SEL
>             Intelligent System in Structure Bioinformatics
>             http://laips.sel.eesc.usp.br
>             Phone: 55 (16) 3373-9366 Ext 229
>             Curriculum Lattes -
>             http://lattes.cnpq.br/1025157978990218
>             Public Profile -
>             http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
> 
>
>             On Mon, Jan 23, 2012 at 11:39 PM, Gianluca
>             Interlandi <gianluca at u.washington.edu> wrote:
>                  Hi!
>
>                  I would like to use gromacs to perform Monte
>             Carlo simulations in implicit
>                  solvent of a protein near a surface. The
>             protein is treated as a rigid body
>                  whereas the surface is fix.
>
>                  I see that there are plans to code MC into
>             gromacs:
>
>                
>              http://www.gromacs.org/Developer_Zone/Programming_Guide/Monte_Carlo
>
>                  Is there a preliminary version?
>
>                  If not, I wonder whether anybody has tried
>             to do MC with gromacs using IMD and
>                  MDDriver:
>
>                  http://www.baaden.ibpc.fr/projects/mddriver/
>
>                  Besides this. Is there an easy way to obtain
>             the force field energy of a system
>                  using gromacs? Would I have to run a 0-steps
>             MD and read out the energy? I know
>                  that this would have a big overhead in a MC
>             simulation, but it might be worth
>                  trying.
>
>                  Thanks,
>
>                      Gianluca
>
>                
>              -----------------------------------------------------
>                  Gianluca Interlandi, PhD
>             gianluca at u.washington.edu
>                                     +1 (206) 685 4435
>                                   
>              http://artemide.bioeng.washington.edu/
>
>                  Postdoc at the Department of Bioengineering
>                  at the University of Washington, Seattle WA
>             U.S.A.
>                
>              -----------------------------------------------------
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> 
> 
>
>       -----------------------------------------------------
>       Gianluca Interlandi, PhD gianluca at u.washington.edu
>                          +1 (206) 685 4435
>                          http://artemide.bioeng.washington.edu/
>
>       Postdoc at the Department of Bioengineering
>       at the University of Washington, Seattle WA U.S.A.
>       -----------------------------------------------------
> 
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>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca at u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------


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