[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.
>>      ------------------------------**-----------------------
>>
>> --
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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.
> ------------------------------**-----------------------
>
> --
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