[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.
>
>                     -----------------------------------------------------
>                         --
>                         gmx-users mailing list
>         gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>
>         http://lists.gromacs.org/mailman/listinfo/gmx-users
>                         Please search the archive at
>
>         http://www.gromacs.org/Support/Mailing_Lists/Search
>                    before posting!
>                         Please don't post (un)subscribe requests to
>                    the list. Use the www interface or
>                         send it to gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>.
>                         Can't post? Read
>         http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
>
>              -----------------------------------------------------
>              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.
>              -----------------------------------------------------
>
>         --
>         gmx-users mailing list gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>         http://lists.gromacs.org/mailman/listinfo/gmx-users
>         Please search the archive at
>         http://www.gromacs.org/Support/Mailing_Lists/Search before
>         posting!
>         Please don't post (un)subscribe requests to the list. Use the
>         www interface or send it to gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>.
>         Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
>
>
>     -----------------------------------------------------
>     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.
>     -----------------------------------------------------
>
>     --
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120130/2390b98e/attachment.html>


More information about the gromacs.org_gmx-users mailing list