[gmx-users] Monte Carlo with Gromacs and implicit solvent
René Pool
r.pool at vu.nl
Mon Jan 30 10:59:12 CET 2012
Hi,
GromPy is compatible with gmx 4.0.7. There are plans to port it to
higher gmx versions, but I do not know when that will happen.
Cheers,
René
=====================================================
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 01/25/2012 06:53 AM, Kiwoong Kim wrote:
> Grompy looks like fancy.
> Is it reliable for conducting GCMC??
>
> I also need to perform GCMC along with MD.
>
> In Grompy, it seems that the Grompy is compatible with gromacs 4.0.5.
> The version of gromacs I use is 4.5.X.
> Is it possible to use Grompy with my Gromacs??
>
>
> 2012/1/25 Gianluca Interlandi <gianluca at u.washington.edu
> <mailto:gianluca at u.washington.edu>>
>
> Hi Renè,
>
> This might be a silly question. In the documentation of GromPy it
> says that:
>
> "The system consists of mono-atomic water molceules defined in the
> MARTINI force field. The intermolecular interactions between such
> molecules are modelled using the Lennard-Jones potential only."
>
> My system is all-atom and all-hydrogen and I need to use the GBSA
> solvation model. Is it still going to work, or is the tutorial
> just an example of what you can do with GromPy?
>
> Thanks,
>
> 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 <mailto: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 <mailto:r.pool at vu.nl>
> T: +31 20 598 76 12
> F: +31 20 598 76 10
> =====================================================
>
> _____________________________________________________________________________________
>
>
> From: gmx-users-bounces at gromacs.org
> <mailto:gmx-users-bounces at gromacs.org>
> [gmx-users-bounces at gromacs.org
> <mailto:gmx-users-bounces at gromacs.org>] on behalf
> of Rodrigo Faccioli [rodrigo_faccioli at uol.com.br
> <mailto: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
>
> 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
> 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
> 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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