[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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