[gmx-users] Monte Carlo with Gromacs and implicit solvent
Kiwoong Kim
ilmarejoe at gmail.com
Wed Jan 25 06:53:27 CET 2012
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>
> 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<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<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<http://lattes.cnpq.br/1025157978990218>
>> Public Profile - http://br.linkedin.com/pub/**rodrigo-faccioli/7/589/a5<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<http://lattes.cnpq.br/1025157978990218>
>> Public Profile -
>> http://br.linkedin.com/pub/**rodrigo-faccioli/7/589/a5<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<http://lattes.cnpq.br/1025157978990218>
>> Public Profile -
>> http://br.linkedin.com/pub/**rodrigo-faccioli/7/589/a5<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<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/<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/<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/<http://artemide.bioeng.washington.edu/>
>>
>> Postdoc at the Department of Bioengineering
>> at the University of Washington, Seattle WA U.S.A.
>> ------------------------------**-----------------------
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
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>>
>>
>>
>>
> ------------------------------**-----------------------
> Gianluca Interlandi, PhD gianluca at u.washington.edu
> +1 (206) 685 4435
> http://artemide.bioeng.**washington.edu/<http://artemide.bioeng.washington.edu/>
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> ------------------------------**-----------------------
>
> --
> gmx-users mailing list gmx-users at gromacs.org
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