[gmx-users] Monte Carlo with Gromacs and implicit solvent
René Pool
r.pool at vu.nl
Tue Jan 24 10:00:34 CET 2012
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 <mailto: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 <mailto: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
> <mailto: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
> <mailto:gianluca at u.washington.edu>
> +1 (206) 685 4435 <tel:%2B1%20%28206%29%20685%204435>
> 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
> <mailto:gianluca at u.washington.edu>
> +1 (206) 685 4435 <tel:%2B1%20%28206%29%20685%204435>
> 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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